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BRCancer

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  1. .gitattributes +89 -0
  2. data/__notebook__.ipynb +3065 -0
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+ "[9438/10000] (0.95GB) Downloading: TCGA-BH-A0E1-11A-01-BSA.92fc4382-6bb1-4ca5-ac90-8116afde7d92.svs (153.50 MB)... "
77881
+ ]
77882
+ },
77883
+ {
77884
+ "name": "stdout",
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+ "output_type": "stream",
77886
+ "text": [
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+ "OK\n",
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+ "[9439/10000] (1.10GB) Downloading: 30dff985-dbda-4e2d-acf3-f91f7f9be56b_noid_Red.idat (7.72 MB)... "
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+ ]
77890
+ },
77891
+ {
77892
+ "name": "stdout",
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+ "output_type": "stream",
77894
+ "text": [
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+ "OK\n",
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+ "[9440/10000] (1.11GB) Downloading: TCGA-BRCA.cf4b7782-45d9-4dfc-b36d-af59befa7c03.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
77897
+ ]
77898
+ },
77899
+ {
77900
+ "name": "stdout",
77901
+ "output_type": "stream",
77902
+ "text": [
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+ "OK\n",
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+ "[9441/10000] (1.11GB) Downloading: nationwidechildrens.org_clinical.TCGA-AR-A1AO.xml (0.09 MB)... "
77905
+ ]
77906
+ },
77907
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
77910
+ "text": [
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+ "OK\n",
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+ "[9442/10000] (1.11GB) Downloading: TCGA-AR-A1AO-01A-11D-A895-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.02 MB)... "
77913
+ ]
77914
+ },
77915
+ {
77916
+ "name": "stdout",
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+ "output_type": "stream",
77918
+ "text": [
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+ "OK\n",
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+ "[9443/10000] (1.11GB) Downloading: 438cb24b-accd-4d4d-8de8-157138091eef_noid_Red.idat (7.72 MB)... "
77921
+ ]
77922
+ },
77923
+ {
77924
+ "name": "stdout",
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+ "output_type": "stream",
77926
+ "text": [
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+ "OK\n",
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+ "[9444/10000] (1.12GB) Downloading: TCGA-BRCA.e18c22cb-6ef7-44c4-8bca-a3d70a3be9ed.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
77929
+ ]
77930
+ },
77931
+ {
77932
+ "name": "stdout",
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+ "output_type": "stream",
77934
+ "text": [
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+ "OK\n",
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+ "[9445/10000] (1.12GB) Downloading: cfba3fd3-4d84-46e6-9c12-8bf8481b35aa.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
77937
+ ]
77938
+ },
77939
+ {
77940
+ "name": "stdout",
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+ "output_type": "stream",
77942
+ "text": [
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+ "OK\n",
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+ "[9446/10000] (1.13GB) Downloading: TCGA-BRCA.e18c22cb-6ef7-44c4-8bca-a3d70a3be9ed.ascat2.allelic_specific.seg.txt (0.01 MB)... "
77945
+ ]
77946
+ },
77947
+ {
77948
+ "name": "stdout",
77949
+ "output_type": "stream",
77950
+ "text": [
77951
+ "OK\n",
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+ "[9447/10000] (1.13GB) Downloading: CELLA_p_TCGA_177_179_Esph_SNP_N_GenomeWideSNP_6_E07_871038.nocnv_grch38.seg.v2.txt (0.00 MB)... "
77953
+ ]
77954
+ },
77955
+ {
77956
+ "name": "stdout",
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+ "output_type": "stream",
77958
+ "text": [
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+ "OK\n",
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+ "[9448/10000] (1.13GB) Downloading: CELLA_p_TCGA_177_179_Esph_SNP_N_GenomeWideSNP_6_E07_871038.grch38.seg.v2.txt (0.02 MB)... "
77961
+ ]
77962
+ },
77963
+ {
77964
+ "name": "stdout",
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+ "output_type": "stream",
77966
+ "text": [
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+ "OK\n",
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+ "[9449/10000] (1.13GB) Downloading: TCGA-A8-A09M-01Z-00-DX1.E2CEA8B5-C86D-4873-BE67-359FBEECCA09.svs (863.02 MB)... "
77969
+ ]
77970
+ },
77971
+ {
77972
+ "name": "stdout",
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+ "output_type": "stream",
77974
+ "text": [
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+ "OK\n",
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+ "[9450/10000] (1.97GB) Downloading: TCGA-BRCA.ebcb8722-05fc-441d-a13a-1fb5c8f1228f.ascat3.allelic_specific.seg.txt (0.00 MB)... "
77977
+ ]
77978
+ },
77979
+ {
77980
+ "name": "stdout",
77981
+ "output_type": "stream",
77982
+ "text": [
77983
+ "OK\n",
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+ "[9451/10000] (1.97GB) Downloading: TCGA-BRCA.cf4b7782-45d9-4dfc-b36d-af59befa7c03.ascat3.allelic_specific.seg.txt (0.00 MB)... "
77985
+ ]
77986
+ },
77987
+ {
77988
+ "name": "stdout",
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+ "output_type": "stream",
77990
+ "text": [
77991
+ "OK\n",
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+ "[9452/10000] (1.97GB) Downloading: cacdfa02-4525-441f-8d63-3324b654a903.mirbase21.isoforms.quantification.txt (0.31 MB)... "
77993
+ ]
77994
+ },
77995
+ {
77996
+ "name": "stdout",
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+ "output_type": "stream",
77998
+ "text": [
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+ "OK\n",
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+ "[9453/10000] (1.97GB) Downloading: TCGA-BH-A0E1-01A-21-A13B-20_RPPA_data.tsv (0.02 MB)... "
78001
+ ]
78002
+ },
78003
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
78006
+ "text": [
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+ "OK\n",
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+ "[9454/10000] (1.97GB) Downloading: TCGA-BRCA.9240c87f-41fc-4576-aedb-2c8010079920.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
78009
+ ]
78010
+ },
78011
+ {
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+ "name": "stdout",
78013
+ "output_type": "stream",
78014
+ "text": [
78015
+ "OK\n",
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+ "[9455/10000] (1.97GB) Downloading: 2832c577-b3a0-42b0-92c9-f7cf6b45fc00.methylation_array.sesame.level3betas.txt (0.73 MB)... "
78017
+ ]
78018
+ },
78019
+ {
78020
+ "name": "stdout",
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+ "output_type": "stream",
78022
+ "text": [
78023
+ "OK\n",
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+ "[9456/10000] (1.97GB) Downloading: TCGA-BRCA.ebcb8722-05fc-441d-a13a-1fb5c8f1228f.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
78025
+ ]
78026
+ },
78027
+ {
78028
+ "name": "stdout",
78029
+ "output_type": "stream",
78030
+ "text": [
78031
+ "OK\n",
78032
+ "[9457/10000] (1.98GB) Downloading: 12da04c4-c74f-480f-9a3f-8c7c421a71f2_noid_Red.idat (0.69 MB)... "
78033
+ ]
78034
+ },
78035
+ {
78036
+ "name": "stdout",
78037
+ "output_type": "stream",
78038
+ "text": [
78039
+ "OK\n",
78040
+ "[9458/10000] (1.98GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A2L8.xml (0.05 MB)... "
78041
+ ]
78042
+ },
78043
+ {
78044
+ "name": "stdout",
78045
+ "output_type": "stream",
78046
+ "text": [
78047
+ "OK\n",
78048
+ "[9459/10000] (1.98GB) Downloading: TCGA-BRCA.ebcb8722-05fc-441d-a13a-1fb5c8f1228f.gene_level_copy_number.v36.tsv (3.29 MB)... "
78049
+ ]
78050
+ },
78051
+ {
78052
+ "name": "stdout",
78053
+ "output_type": "stream",
78054
+ "text": [
78055
+ "OK\n",
78056
+ "[9460/10000] (1.98GB) Downloading: TCGA-BRCA.9240c87f-41fc-4576-aedb-2c8010079920.ascat2.allelic_specific.seg.txt (0.01 MB)... "
78057
+ ]
78058
+ },
78059
+ {
78060
+ "name": "stdout",
78061
+ "output_type": "stream",
78062
+ "text": [
78063
+ "OK\n",
78064
+ "[9461/10000] (1.98GB) Downloading: f988afae-48f8-4ecc-bb84-87924b454bf0.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
78065
+ ]
78066
+ },
78067
+ {
78068
+ "name": "stdout",
78069
+ "output_type": "stream",
78070
+ "text": [
78071
+ "OK\n",
78072
+ "[9462/10000] (1.98GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_D04_697026.grch38.seg.v2.txt (0.04 MB)... "
78073
+ ]
78074
+ },
78075
+ {
78076
+ "name": "stdout",
78077
+ "output_type": "stream",
78078
+ "text": [
78079
+ "OK\n",
78080
+ "[9463/10000] (1.99GB) Downloading: TCGA-BRCA.06007408-83ae-42dd-b7ea-bd017e97669f.ascat3.allelic_specific.seg.txt (0.01 MB)... "
78081
+ ]
78082
+ },
78083
+ {
78084
+ "name": "stdout",
78085
+ "output_type": "stream",
78086
+ "text": [
78087
+ "OK\n",
78088
+ "[9464/10000] (1.99GB) Downloading: nationwidechildrens.org_clinical.TCGA-D8-A1JI.xml (0.08 MB)... "
78089
+ ]
78090
+ },
78091
+ {
78092
+ "name": "stdout",
78093
+ "output_type": "stream",
78094
+ "text": [
78095
+ "OK\n",
78096
+ "[9465/10000] (1.99GB) Downloading: 12da04c4-c74f-480f-9a3f-8c7c421a71f2_noid_Grn.idat (0.69 MB)... "
78097
+ ]
78098
+ },
78099
+ {
78100
+ "name": "stdout",
78101
+ "output_type": "stream",
78102
+ "text": [
78103
+ "OK\n",
78104
+ "[9466/10000] (1.99GB) Downloading: 30dff985-dbda-4e2d-acf3-f91f7f9be56b_noid_Grn.idat (7.72 MB)... "
78105
+ ]
78106
+ },
78107
+ {
78108
+ "name": "stdout",
78109
+ "output_type": "stream",
78110
+ "text": [
78111
+ "OK\n",
78112
+ "[9467/10000] (1.99GB) Downloading: TCGA-A8-A0A1-01A-01-TS1.eb96c625-348f-4355-a9d2-7e44853a1888.svs (399.96 MB)... "
78113
+ ]
78114
+ },
78115
+ {
78116
+ "name": "stdout",
78117
+ "output_type": "stream",
78118
+ "text": [
78119
+ "OK\n",
78120
+ "[9468/10000] (2.38GB) Downloading: TCGA-BRCA.06007408-83ae-42dd-b7ea-bd017e97669f.ascat2.allelic_specific.seg.txt (0.01 MB)... "
78121
+ ]
78122
+ },
78123
+ {
78124
+ "name": "stdout",
78125
+ "output_type": "stream",
78126
+ "text": [
78127
+ "OK\n",
78128
+ "[9469/10000] (2.38GB) Downloading: TCGA-D8-A1JI-01A-11D-A897-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.13 MB)... "
78129
+ ]
78130
+ },
78131
+ {
78132
+ "name": "stdout",
78133
+ "output_type": "stream",
78134
+ "text": [
78135
+ "OK\n",
78136
+ "[9470/10000] (2.38GB) Downloading: ac3ccdb6-84ee-43d7-afc4-8172e387b138.mirbase21.isoforms.quantification.txt (0.28 MB)... "
78137
+ ]
78138
+ },
78139
+ {
78140
+ "name": "stdout",
78141
+ "output_type": "stream",
78142
+ "text": [
78143
+ "OK\n",
78144
+ "[9471/10000] (2.38GB) Downloading: TCGA-A8-A09M-01A-01-TSA.d3865338-2456-4943-93b3-7bf1e3749684.svs (456.24 MB)... "
78145
+ ]
78146
+ },
78147
+ {
78148
+ "name": "stdout",
78149
+ "output_type": "stream",
78150
+ "text": [
78151
+ "OK\n",
78152
+ "[9472/10000] (2.83GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_F06_772080.nocnv_grch38.seg.v2.txt (0.00 MB)... "
78153
+ ]
78154
+ },
78155
+ {
78156
+ "name": "stdout",
78157
+ "output_type": "stream",
78158
+ "text": [
78159
+ "OK\n",
78160
+ "[9473/10000] (2.83GB) Downloading: fd5ccaf6-e9be-4be2-99f7-606d1bbbf3de.mirbase21.mirnas.quantification.txt (0.05 MB)... "
78161
+ ]
78162
+ },
78163
+ {
78164
+ "name": "stdout",
78165
+ "output_type": "stream",
78166
+ "text": [
78167
+ "OK\n",
78168
+ "[9474/10000] (2.83GB) Downloading: nationwidechildrens.org_ssf.TCGA-BH-A0E1.xml (0.02 MB)... "
78169
+ ]
78170
+ },
78171
+ {
78172
+ "name": "stdout",
78173
+ "output_type": "stream",
78174
+ "text": [
78175
+ "OK\n",
78176
+ "[9475/10000] (2.83GB) Downloading: TCGA-BRCA.a2a1f3e8-7484-4105-92b6-6a7d0b2d9ace.gene_level_copy_number.v36.tsv (3.29 MB)... "
78177
+ ]
78178
+ },
78179
+ {
78180
+ "name": "stdout",
78181
+ "output_type": "stream",
78182
+ "text": [
78183
+ "OK\n",
78184
+ "[9476/10000] (2.83GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_E05_772196.grch38.seg.v2.txt (0.04 MB)... "
78185
+ ]
78186
+ },
78187
+ {
78188
+ "name": "stdout",
78189
+ "output_type": "stream",
78190
+ "text": [
78191
+ "OK\n",
78192
+ "[9477/10000] (2.83GB) Downloading: TCGA-D8-A1J8-01A-11D-A897-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.14 MB)... "
78193
+ ]
78194
+ },
78195
+ {
78196
+ "name": "stdout",
78197
+ "output_type": "stream",
78198
+ "text": [
78199
+ "OK\n",
78200
+ "[9478/10000] (2.83GB) Downloading: b60aae02-5a04-4ee4-85ac-338a38b9c6ea.mirbase21.isoforms.quantification.txt (0.37 MB)... "
78201
+ ]
78202
+ },
78203
+ {
78204
+ "name": "stdout",
78205
+ "output_type": "stream",
78206
+ "text": [
78207
+ "OK\n",
78208
+ "[9479/10000] (2.83GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_E05_772196.nocnv_grch38.seg.v2.txt (0.02 MB)... "
78209
+ ]
78210
+ },
78211
+ {
78212
+ "name": "stdout",
78213
+ "output_type": "stream",
78214
+ "text": [
78215
+ "OK\n",
78216
+ "[9480/10000] (2.83GB) Downloading: 1e635971-2d16-4be0-bc3f-4ce6a48ee23f_noid_Grn.idat (7.72 MB)... "
78217
+ ]
78218
+ },
78219
+ {
78220
+ "name": "stdout",
78221
+ "output_type": "stream",
78222
+ "text": [
78223
+ "OK\n",
78224
+ "[9481/10000] (2.84GB) Downloading: 74039acd-5aca-4c65-818c-3b577d295be0_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.09 MB)... "
78225
+ ]
78226
+ },
78227
+ {
78228
+ "name": "stdout",
78229
+ "output_type": "stream",
78230
+ "text": [
78231
+ "OK\n",
78232
+ "[9482/10000] (2.84GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-D8-A1J8.xml (0.06 MB)... "
78233
+ ]
78234
+ },
78235
+ {
78236
+ "name": "stdout",
78237
+ "output_type": "stream",
78238
+ "text": [
78239
+ "OK\n",
78240
+ "[9483/10000] (2.84GB) Downloading: TCGA-D8-A1JI-01Z-00-DX2.E688E270-26C9-43EC-BC26-86BF8B74A31D.svs (943.61 MB)... "
78241
+ ]
78242
+ },
78243
+ {
78244
+ "name": "stdout",
78245
+ "output_type": "stream",
78246
+ "text": [
78247
+ "OK\n",
78248
+ "[9484/10000] (3.76GB) Downloading: nationwidechildrens.org_clinical.TCGA-E9-A1RH.xml (0.11 MB)... "
78249
+ ]
78250
+ },
78251
+ {
78252
+ "name": "stdout",
78253
+ "output_type": "stream",
78254
+ "text": [
78255
+ "OK\n",
78256
+ "[9485/10000] (3.76GB) Downloading: TCGA-BRCA.83255030-c4f5-48ed-829b-3b06dd57adbb.ascat3.allelic_specific.seg.txt (0.00 MB)... "
78257
+ ]
78258
+ },
78259
+ {
78260
+ "name": "stdout",
78261
+ "output_type": "stream",
78262
+ "text": [
78263
+ "OK\n",
78264
+ "[9486/10000] (3.76GB) Downloading: TCGA-AN-A0FT-01A-01-TSA.d6fe3f83-5cbc-4c39-ad49-c3adfee44974.svs (364.27 MB)... "
78265
+ ]
78266
+ },
78267
+ {
78268
+ "name": "stdout",
78269
+ "output_type": "stream",
78270
+ "text": [
78271
+ "OK\n",
78272
+ "[9487/10000] (4.12GB) Downloading: TCGA-E9-A1RH-01A-02-TSB.03b969da-c200-48e2-bed2-ec2830daf487.svs (229.68 MB)... "
78273
+ ]
78274
+ },
78275
+ {
78276
+ "name": "stdout",
78277
+ "output_type": "stream",
78278
+ "text": [
78279
+ "OK\n",
78280
+ "[9488/10000] (4.34GB) Downloading: TCGA-BRCA.83255030-c4f5-48ed-829b-3b06dd57adbb.gene_level_copy_number.v36.tsv (3.29 MB)... "
78281
+ ]
78282
+ },
78283
+ {
78284
+ "name": "stdout",
78285
+ "output_type": "stream",
78286
+ "text": [
78287
+ "OK\n",
78288
+ "[9489/10000] (4.35GB) Downloading: TCGA-BRCA.de88f4c3-0824-4ce2-8d1c-c6155db0f967.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
78289
+ ]
78290
+ },
78291
+ {
78292
+ "name": "stdout",
78293
+ "output_type": "stream",
78294
+ "text": [
78295
+ "OK\n",
78296
+ "[9490/10000] (4.35GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_A09_735258.nocnv_grch38.seg.v2.txt (0.00 MB)... "
78297
+ ]
78298
+ },
78299
+ {
78300
+ "name": "stdout",
78301
+ "output_type": "stream",
78302
+ "text": [
78303
+ "OK\n",
78304
+ "[9491/10000] (4.35GB) Downloading: 8df50c7b-93ce-498d-bca2-fae60069fd3e_noid_Grn.idat (7.72 MB)... "
78305
+ ]
78306
+ },
78307
+ {
78308
+ "name": "stdout",
78309
+ "output_type": "stream",
78310
+ "text": [
78311
+ "OK\n",
78312
+ "[9492/10000] (4.36GB) Downloading: 7d746ed3-9bfa-4f66-9c5a-594284ecd811.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
78313
+ ]
78314
+ },
78315
+ {
78316
+ "name": "stdout",
78317
+ "output_type": "stream",
78318
+ "text": [
78319
+ "OK\n",
78320
+ "[9493/10000] (4.36GB) Downloading: TCGA-D8-A1J8.E8E799F8-158D-4AEC-8F86-D40F132C071C.PDF (0.07 MB)... "
78321
+ ]
78322
+ },
78323
+ {
78324
+ "name": "stdout",
78325
+ "output_type": "stream",
78326
+ "text": [
78327
+ "OK\n",
78328
+ "[9494/10000] (4.36GB) Downloading: TCGA-E9-A1RH-11A-01-TSA.ac96d612-a880-4bca-9248-8206b9022b8a.svs (58.43 MB)... "
78329
+ ]
78330
+ },
78331
+ {
78332
+ "name": "stdout",
78333
+ "output_type": "stream",
78334
+ "text": [
78335
+ "OK\n",
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "text": [
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+ "OK\n",
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9498/10000] (4.42GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_C01_772134.nocnv_grch38.seg.v2.txt (0.01 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9500/10000] (4.42GB) Downloading: nationwidechildrens.org_ssf.TCGA-GM-A4E0.xml (0.01 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9501/10000] (4.42GB) Downloading: 3d019f9a-1a93-4602-aefb-71ff0f011032_noid_Grn.idat (0.69 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9502/10000] (4.42GB) Downloading: TCGA-E9-A1RH.FA93BDAA-B56E-4217-9022-4EBE6009FCF7.PDF (0.06 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9503/10000] (4.42GB) Downloading: TCGA-E2-A14X-01A-11D-A895-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.07 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9504/10000] (4.42GB) Downloading: TCGA-BRCA.323df895-a6a9-4fd1-9aab-6ae770381071.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9505/10000] (4.43GB) Downloading: d0ee5ff7-a49a-4633-93a6-40c9e29fb0b7.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9506/10000] (4.43GB) Downloading: nationwidechildrens.org_clinical.TCGA-E9-A22B.xml (0.08 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9507/10000] (4.43GB) Downloading: 0a8d531c-db3a-4752-9339-6ed531694305_noid_Red.idat (7.72 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9508/10000] (4.44GB) Downloading: 466a4121-0583-47ee-9d54-1f1c2d47e381.rna_seq.augmented_star_gene_counts.tsv (4.07 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9509/10000] (4.44GB) Downloading: TCGA-BRCA.323df895-a6a9-4fd1-9aab-6ae770381071.ascat2.allelic_specific.seg.txt (0.01 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9510/10000] (4.44GB) Downloading: TCGA-BRCA.260ee6fb-7c05-41d7-93c4-8c5c5e40f5ff.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
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+ ]
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+ },
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+ {
78460
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9511/10000] (4.44GB) Downloading: TCGA-GM-A4E0-01A-01-TS1.43B57619-CB29-46C6-BAEA-5064872B4EE7.svs (109.93 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9512/10000] (4.55GB) Downloading: 91151f2d-1b98-4671-8e79-05e07931e325.mirbase21.mirnas.quantification.txt (0.05 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9513/10000] (4.55GB) Downloading: TCGA-AR-A2LQ.C3537961-4636-4BD1-BC89-892580B36E43.PDF (0.10 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9514/10000] (4.55GB) Downloading: CELLA_p_TCGA_177_179_Esph_SNP_N_GenomeWideSNP_6_A10_871076.grch38.seg.v2.txt (0.03 MB)... "
78489
+ ]
78490
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9515/10000] (4.55GB) Downloading: TCGA-BRCA.895c4a2a-2c43-4e3a-ab26-694f80b7ca70.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
78497
+ ]
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+ },
78499
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9516/10000] (4.55GB) Downloading: TCGA-E2-A573-01Z-00-DX1.D6633BC2-524D-4153-952F-6B1D8D067370.svs (1189.64 MB)... "
78505
+ ]
78506
+ },
78507
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
78510
+ "text": [
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+ "OK\n",
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+ "[9517/10000] (5.72GB) Downloading: TCGA-BRCA.150d0521-0135-44b1-b5c5-635050b30973.gene_level_copy_number.v36.tsv (3.29 MB)... "
78513
+ ]
78514
+ },
78515
+ {
78516
+ "name": "stdout",
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+ "output_type": "stream",
78518
+ "text": [
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+ "OK\n",
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+ "[9518/10000] (5.72GB) Downloading: fb67df9a-6338-4305-9d8f-47f22d0692c4_noid_Red.idat (7.72 MB)... "
78521
+ ]
78522
+ },
78523
+ {
78524
+ "name": "stdout",
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+ "output_type": "stream",
78526
+ "text": [
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+ "OK\n",
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+ "[9519/10000] (5.73GB) Downloading: 1daa0996-c123-4067-a397-caa3e6e911d7_noid_Red.idat (7.72 MB)... "
78529
+ ]
78530
+ },
78531
+ {
78532
+ "name": "stdout",
78533
+ "output_type": "stream",
78534
+ "text": [
78535
+ "OK\n",
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+ "[9520/10000] (5.73GB) Downloading: RANDS_p_TCGA_b109_SNP_1N_GenomeWideSNP_6_E06_771948.nocnv_grch38.seg.v2.txt (0.01 MB)... "
78537
+ ]
78538
+ },
78539
+ {
78540
+ "name": "stdout",
78541
+ "output_type": "stream",
78542
+ "text": [
78543
+ "OK\n",
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+ "[9521/10000] (5.73GB) Downloading: dde887a7-33ba-4274-9583-45c20e41d213.mirbase21.mirnas.quantification.txt (0.05 MB)... "
78545
+ ]
78546
+ },
78547
+ {
78548
+ "name": "stdout",
78549
+ "output_type": "stream",
78550
+ "text": [
78551
+ "OK\n",
78552
+ "[9522/10000] (5.73GB) Downloading: 412b96f4-4463-49ab-aee6-78b3859e7b70.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
78553
+ ]
78554
+ },
78555
+ {
78556
+ "name": "stdout",
78557
+ "output_type": "stream",
78558
+ "text": [
78559
+ "OK\n",
78560
+ "[9523/10000] (5.74GB) Downloading: nationwidechildrens.org_clinical.TCGA-AR-A0TV.xml (0.06 MB)... "
78561
+ ]
78562
+ },
78563
+ {
78564
+ "name": "stdout",
78565
+ "output_type": "stream",
78566
+ "text": [
78567
+ "OK\n",
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+ "[9524/10000] (5.74GB) Downloading: TCGA-BRCA.895c4a2a-2c43-4e3a-ab26-694f80b7ca70.gene_level_copy_number.v36.tsv (3.29 MB)... "
78569
+ ]
78570
+ },
78571
+ {
78572
+ "name": "stdout",
78573
+ "output_type": "stream",
78574
+ "text": [
78575
+ "OK\n",
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+ "[9525/10000] (5.74GB) Downloading: 789cf53d-e3ea-4ad0-bd57-d40b8348e5ff.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
78577
+ ]
78578
+ },
78579
+ {
78580
+ "name": "stdout",
78581
+ "output_type": "stream",
78582
+ "text": [
78583
+ "OK\n",
78584
+ "[9526/10000] (5.74GB) Downloading: 86e20e42-8755-46df-907f-3f755e9b50fb_noid_Red.idat (7.72 MB)... "
78585
+ ]
78586
+ },
78587
+ {
78588
+ "name": "stdout",
78589
+ "output_type": "stream",
78590
+ "text": [
78591
+ "OK\n",
78592
+ "[9527/10000] (5.75GB) Downloading: TCGA-BRCA.e06babf2-ca3c-4bde-9c36-9799e305c520.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
78593
+ ]
78594
+ },
78595
+ {
78596
+ "name": "stdout",
78597
+ "output_type": "stream",
78598
+ "text": [
78599
+ "OK\n",
78600
+ "[9528/10000] (5.75GB) Downloading: nationwidechildrens.org_ssf.TCGA-AR-A2LQ.xml (0.02 MB)... "
78601
+ ]
78602
+ },
78603
+ {
78604
+ "name": "stdout",
78605
+ "output_type": "stream",
78606
+ "text": [
78607
+ "OK\n",
78608
+ "[9529/10000] (5.75GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_A10_698106.grch38.seg.v2.txt (0.06 MB)... "
78609
+ ]
78610
+ },
78611
+ {
78612
+ "name": "stdout",
78613
+ "output_type": "stream",
78614
+ "text": [
78615
+ "OK\n",
78616
+ "[9530/10000] (5.75GB) Downloading: TCGA-BRCA.6d730c4d-2c62-4214-aa35-f40126e65560.ascat3.allelic_specific.seg.txt (0.01 MB)... "
78617
+ ]
78618
+ },
78619
+ {
78620
+ "name": "stdout",
78621
+ "output_type": "stream",
78622
+ "text": [
78623
+ "OK\n",
78624
+ "[9531/10000] (5.75GB) Downloading: b6083f69-1744-4ce5-8912-d70c9554d55a_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.08 MB)... "
78625
+ ]
78626
+ },
78627
+ {
78628
+ "name": "stdout",
78629
+ "output_type": "stream",
78630
+ "text": [
78631
+ "OK\n",
78632
+ "[9532/10000] (5.75GB) Downloading: TCGA-BRCA.5f623237-b478-4bca-8647-d633e9e63d7c.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
78633
+ ]
78634
+ },
78635
+ {
78636
+ "name": "stdout",
78637
+ "output_type": "stream",
78638
+ "text": [
78639
+ "OK\n",
78640
+ "[9533/10000] (5.76GB) Downloading: TCGA-BRCA.6d730c4d-2c62-4214-aa35-f40126e65560.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
78641
+ ]
78642
+ },
78643
+ {
78644
+ "name": "stdout",
78645
+ "output_type": "stream",
78646
+ "text": [
78647
+ "OK\n",
78648
+ "[9534/10000] (5.76GB) Downloading: b617d9fc-0048-46ae-b703-b19200168d00.mirbase21.isoforms.quantification.txt (0.24 MB)... "
78649
+ ]
78650
+ },
78651
+ {
78652
+ "name": "stdout",
78653
+ "output_type": "stream",
78654
+ "text": [
78655
+ "OK\n",
78656
+ "[9535/10000] (5.76GB) Downloading: TCGA-BRCA.ad305034-cc87-4557-9031-a50710646810.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
78657
+ ]
78658
+ },
78659
+ {
78660
+ "name": "stdout",
78661
+ "output_type": "stream",
78662
+ "text": [
78663
+ "OK\n",
78664
+ "[9536/10000] (5.76GB) Downloading: TCGA-C8-A12Z-01A-01-TSA.d85a700f-8886-4b59-8ceb-d1d8e15fdd19.svs (204.26 MB)... "
78665
+ ]
78666
+ },
78667
+ {
78668
+ "name": "stdout",
78669
+ "output_type": "stream",
78670
+ "text": [
78671
+ "OK\n",
78672
+ "[9537/10000] (5.96GB) Downloading: TCGA-C8-A12Z-01Z-00-DX1.22616420-7C80-42DE-9C44-0F00327681C6.svs (957.06 MB)... "
78673
+ ]
78674
+ },
78675
+ {
78676
+ "name": "stdout",
78677
+ "output_type": "stream",
78678
+ "text": [
78679
+ "OK\n",
78680
+ "[9538/10000] (6.90GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A2-A0SW.xml (0.08 MB)... "
78681
+ ]
78682
+ },
78683
+ {
78684
+ "name": "stdout",
78685
+ "output_type": "stream",
78686
+ "text": [
78687
+ "OK\n",
78688
+ "[9539/10000] (6.90GB) Downloading: TCGA-C8-A12U-01A-21-A13D-20_RPPA_data.tsv (0.02 MB)... "
78689
+ ]
78690
+ },
78691
+ {
78692
+ "name": "stdout",
78693
+ "output_type": "stream",
78694
+ "text": [
78695
+ "OK\n",
78696
+ "[9540/10000] (6.90GB) Downloading: TCGA-C8-A12Z-01A-31D-A892-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.09 MB)... "
78697
+ ]
78698
+ },
78699
+ {
78700
+ "name": "stdout",
78701
+ "output_type": "stream",
78702
+ "text": [
78703
+ "OK\n",
78704
+ "[9541/10000] (6.90GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_H03_735338.grch38.seg.v2.txt (0.06 MB)... "
78705
+ ]
78706
+ },
78707
+ {
78708
+ "name": "stdout",
78709
+ "output_type": "stream",
78710
+ "text": [
78711
+ "OK\n",
78712
+ "[9542/10000] (6.90GB) Downloading: nationwidechildrens.org_clinical.TCGA-C8-A12U.xml (0.05 MB)... "
78713
+ ]
78714
+ },
78715
+ {
78716
+ "name": "stdout",
78717
+ "output_type": "stream",
78718
+ "text": [
78719
+ "OK\n",
78720
+ "[9543/10000] (6.90GB) Downloading: 062ca805-bac4-4f3d-98dc-92c03f8996c0.methylation_array.sesame.level3betas.txt (0.73 MB)... "
78721
+ ]
78722
+ },
78723
+ {
78724
+ "name": "stdout",
78725
+ "output_type": "stream",
78726
+ "text": [
78727
+ "OK\n",
78728
+ "[9544/10000] (6.90GB) Downloading: TCGA-BRCA.ad305034-cc87-4557-9031-a50710646810.gene_level_copy_number.v36.tsv (3.29 MB)... "
78729
+ ]
78730
+ },
78731
+ {
78732
+ "name": "stdout",
78733
+ "output_type": "stream",
78734
+ "text": [
78735
+ "OK\n",
78736
+ "[9545/10000] (6.90GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-C8-A12Z.xml (0.06 MB)... "
78737
+ ]
78738
+ },
78739
+ {
78740
+ "name": "stdout",
78741
+ "output_type": "stream",
78742
+ "text": [
78743
+ "OK\n",
78744
+ "[9546/10000] (6.90GB) Downloading: TCGA-C8-A12Z.89B312D1-9FDD-4756-9C15-5442B428F75A.PDF (0.22 MB)... "
78745
+ ]
78746
+ },
78747
+ {
78748
+ "name": "stdout",
78749
+ "output_type": "stream",
78750
+ "text": [
78751
+ "OK\n",
78752
+ "[9547/10000] (6.90GB) Downloading: TCGA-C8-A12Z-01A-01-BSA.e7ddd80e-4b44-49f3-ac1c-4cf2b061c0a6.svs (535.86 MB)... "
78753
+ ]
78754
+ },
78755
+ {
78756
+ "name": "stdout",
78757
+ "output_type": "stream",
78758
+ "text": [
78759
+ "OK\n",
78760
+ "[9548/10000] (7.42GB) Downloading: TCGA-AR-A0TV-01A-02-BSB.e4adf5bf-398f-402f-997e-7b5ef9facbe8.svs (135.42 MB)... "
78761
+ ]
78762
+ },
78763
+ {
78764
+ "name": "stdout",
78765
+ "output_type": "stream",
78766
+ "text": [
78767
+ "OK\n",
78768
+ "[9549/10000] (7.56GB) Downloading: TCGA-BRCA.b8ff6277-3c53-4912-ae50-8e82a94f7244.ascat3.allelic_specific.seg.txt (0.01 MB)... "
78769
+ ]
78770
+ },
78771
+ {
78772
+ "name": "stdout",
78773
+ "output_type": "stream",
78774
+ "text": [
78775
+ "OK\n",
78776
+ "[9550/10000] (7.56GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_F07_747934.grch38.seg.v2.txt (0.06 MB)... "
78777
+ ]
78778
+ },
78779
+ {
78780
+ "name": "stdout",
78781
+ "output_type": "stream",
78782
+ "text": [
78783
+ "OK\n",
78784
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+ ]
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+ },
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+ {
78788
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9552/10000] (7.56GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A0BR.xml (0.06 MB)... "
78793
+ ]
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+ },
78795
+ {
78796
+ "name": "stdout",
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+ "output_type": "stream",
78798
+ "text": [
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+ "OK\n",
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+ "[9553/10000] (7.56GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_G10_735244.nocnv_grch38.seg.v2.txt (0.03 MB)... "
78801
+ ]
78802
+ },
78803
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
78806
+ "text": [
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+ "OK\n",
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+ "[9554/10000] (7.56GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_B03_698024.nocnv_grch38.seg.v2.txt (0.02 MB)... "
78809
+ ]
78810
+ },
78811
+ {
78812
+ "name": "stdout",
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+ "output_type": "stream",
78814
+ "text": [
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+ "OK\n",
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+ "[9555/10000] (7.56GB) Downloading: nationwidechildrens.org_clinical.TCGA-C8-A133.xml (0.04 MB)... "
78817
+ ]
78818
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9556/10000] (7.56GB) Downloading: TCGA-AR-A1AI.F5CAE962-5347-46FA-86EE-169121BED547.PDF (0.05 MB)... "
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+ ]
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+ },
78827
+ {
78828
+ "name": "stdout",
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+ "output_type": "stream",
78830
+ "text": [
78831
+ "OK\n",
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+ "[9557/10000] (7.56GB) Downloading: 969cd5a9-33f4-4ac5-ab13-4501abe40576.mirbase21.isoforms.quantification.txt (0.23 MB)... "
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+ ]
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+ },
78835
+ {
78836
+ "name": "stdout",
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+ "output_type": "stream",
78838
+ "text": [
78839
+ "OK\n",
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+ "[9558/10000] (7.56GB) Downloading: b6d49850-d282-4322-a5e1-eceb502050bb_noid_Grn.idat (0.69 MB)... "
78841
+ ]
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+ },
78843
+ {
78844
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9559/10000] (7.56GB) Downloading: TCGA-A2-A0SW-01A-21-A13A-20_RPPA_data.tsv (0.02 MB)... "
78849
+ ]
78850
+ },
78851
+ {
78852
+ "name": "stdout",
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+ "output_type": "stream",
78854
+ "text": [
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+ "OK\n",
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+ "[9560/10000] (7.56GB) Downloading: 9c1bb2f4-455a-445d-ab48-fb64d71c2a52.wgs.ASCAT.copy_number_variation.seg.txt (0.01 MB)... "
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+ ]
78858
+ },
78859
+ {
78860
+ "name": "stdout",
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+ "output_type": "stream",
78862
+ "text": [
78863
+ "OK\n",
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+ "[9561/10000] (7.56GB) Downloading: TCGA-BRCA.68564280-daf0-4bbb-9aa0-79493b39231b.ascat3.allelic_specific.seg.txt (0.01 MB)... "
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+ ]
78866
+ },
78867
+ {
78868
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9562/10000] (7.56GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AR-A1AI.xml (0.06 MB)... "
78873
+ ]
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+ },
78875
+ {
78876
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9563/10000] (7.56GB) Downloading: 5c5bef11-bd78-46e0-a926-ce66bb2ed021.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
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+ ]
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+ },
78883
+ {
78884
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
78887
+ "OK\n",
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+ "[9564/10000] (7.56GB) Downloading: TCGA-BRCA.68564280-daf0-4bbb-9aa0-79493b39231b.gene_level_copy_number.v36.tsv (3.29 MB)... "
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+ ]
78890
+ },
78891
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
78895
+ "OK\n",
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+ "[9565/10000] (7.56GB) Downloading: TCGA-BRCA.deedcd96-88fd-445e-bc6c-085c79a431ab.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
78897
+ ]
78898
+ },
78899
+ {
78900
+ "name": "stdout",
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+ "output_type": "stream",
78902
+ "text": [
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+ "OK\n",
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+ "[9566/10000] (7.56GB) Downloading: TCGA-A8-A094.85288EC6-0BDC-4955-8B88-1DEECBF0E235.PDF (0.04 MB)... "
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+ ]
78906
+ },
78907
+ {
78908
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9567/10000] (7.56GB) Downloading: TCGA-BRCA.deedcd96-88fd-445e-bc6c-085c79a431ab.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
78913
+ ]
78914
+ },
78915
+ {
78916
+ "name": "stdout",
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+ "output_type": "stream",
78918
+ "text": [
78919
+ "OK\n",
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+ "[9568/10000] (7.57GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_A08_741564.grch38.seg.v2.txt (0.03 MB)... "
78921
+ ]
78922
+ },
78923
+ {
78924
+ "name": "stdout",
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+ "output_type": "stream",
78926
+ "text": [
78927
+ "OK\n",
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+ "[9569/10000] (7.57GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H03_628502.nocnv_grch38.seg.v2.txt (0.03 MB)... "
78929
+ ]
78930
+ },
78931
+ {
78932
+ "name": "stdout",
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+ "output_type": "stream",
78934
+ "text": [
78935
+ "OK\n",
78936
+ "[9570/10000] (7.57GB) Downloading: 6dd29ab4-e269-429b-abd7-a71b5c5991ff.wgs.ASCAT.gene_level.copy_number_variation.tsv (3.28 MB)... "
78937
+ ]
78938
+ },
78939
+ {
78940
+ "name": "stdout",
78941
+ "output_type": "stream",
78942
+ "text": [
78943
+ "OK\n",
78944
+ "[9571/10000] (7.57GB) Downloading: 20658f84-7e36-440f-9e88-08eab304813b.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
78945
+ ]
78946
+ },
78947
+ {
78948
+ "name": "stdout",
78949
+ "output_type": "stream",
78950
+ "text": [
78951
+ "OK\n",
78952
+ "[9572/10000] (7.58GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_F07_747934.nocnv_grch38.seg.v2.txt (0.04 MB)... "
78953
+ ]
78954
+ },
78955
+ {
78956
+ "name": "stdout",
78957
+ "output_type": "stream",
78958
+ "text": [
78959
+ "OK\n",
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+ "[9573/10000] (7.58GB) Downloading: d8cc0309-4e61-4921-9b66-4483277afcf4_noid_Grn.idat (7.72 MB)... "
78961
+ ]
78962
+ },
78963
+ {
78964
+ "name": "stdout",
78965
+ "output_type": "stream",
78966
+ "text": [
78967
+ "OK\n",
78968
+ "[9574/10000] (7.58GB) Downloading: TCGA-BRCA.568de015-d66d-4731-83ce-8f8439ffa6b2.ascat3.allelic_specific.seg.txt (0.00 MB)... "
78969
+ ]
78970
+ },
78971
+ {
78972
+ "name": "stdout",
78973
+ "output_type": "stream",
78974
+ "text": [
78975
+ "OK\n",
78976
+ "[9575/10000] (7.58GB) Downloading: 254e6e3e-e30e-46c3-890a-18df11361eac_noid_Grn.idat (7.72 MB)... "
78977
+ ]
78978
+ },
78979
+ {
78980
+ "name": "stdout",
78981
+ "output_type": "stream",
78982
+ "text": [
78983
+ "OK\n",
78984
+ "[9576/10000] (7.59GB) Downloading: ce7471cc-a727-42bb-bded-e4a657e5b8fb.mirbase21.isoforms.quantification.txt (0.34 MB)... "
78985
+ ]
78986
+ },
78987
+ {
78988
+ "name": "stdout",
78989
+ "output_type": "stream",
78990
+ "text": [
78991
+ "OK\n",
78992
+ "[9577/10000] (7.59GB) Downloading: TCGA-BRCA.568de015-d66d-4731-83ce-8f8439ffa6b2.ascat2.allelic_specific.seg.txt (0.01 MB)... "
78993
+ ]
78994
+ },
78995
+ {
78996
+ "name": "stdout",
78997
+ "output_type": "stream",
78998
+ "text": [
78999
+ "OK\n",
79000
+ "[9578/10000] (7.59GB) Downloading: TCGA-A8-A094-01A-01-BS1.f21f55c9-cd4c-4677-ba95-bfe2e6a5ee0d.svs (196.81 MB)... "
79001
+ ]
79002
+ },
79003
+ {
79004
+ "name": "stdout",
79005
+ "output_type": "stream",
79006
+ "text": [
79007
+ "OK\n",
79008
+ "[9579/10000] (7.78GB) Downloading: nationwidechildrens.org_ssf.TCGA-B6-A2IU.xml (0.01 MB)... "
79009
+ ]
79010
+ },
79011
+ {
79012
+ "name": "stdout",
79013
+ "output_type": "stream",
79014
+ "text": [
79015
+ "OK\n",
79016
+ "[9580/10000] (7.78GB) Downloading: a4397eb3-c9ce-4af7-96cf-75a7bb4bcbbc.mirbase21.mirnas.quantification.txt (0.05 MB)... "
79017
+ ]
79018
+ },
79019
+ {
79020
+ "name": "stdout",
79021
+ "output_type": "stream",
79022
+ "text": [
79023
+ "OK\n",
79024
+ "[9581/10000] (7.78GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_A07_628480.nocnv_grch38.seg.v2.txt (0.01 MB)... "
79025
+ ]
79026
+ },
79027
+ {
79028
+ "name": "stdout",
79029
+ "output_type": "stream",
79030
+ "text": [
79031
+ "OK\n",
79032
+ "[9582/10000] (7.78GB) Downloading: f82b3de1-58a4-47b7-bf32-388098bba46f_noid_Red.idat (0.69 MB)... "
79033
+ ]
79034
+ },
79035
+ {
79036
+ "name": "stdout",
79037
+ "output_type": "stream",
79038
+ "text": [
79039
+ "OK\n",
79040
+ "[9583/10000] (7.78GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H03_628502.grch38.seg.v2.txt (0.07 MB)... "
79041
+ ]
79042
+ },
79043
+ {
79044
+ "name": "stdout",
79045
+ "output_type": "stream",
79046
+ "text": [
79047
+ "OK\n",
79048
+ "[9584/10000] (7.78GB) Downloading: CELLA_p_TCGA_177_179_Esph_SNP_N_GenomeWideSNP_6_D10_871018.grch38.seg.v2.txt (0.03 MB)... "
79049
+ ]
79050
+ },
79051
+ {
79052
+ "name": "stdout",
79053
+ "output_type": "stream",
79054
+ "text": [
79055
+ "OK\n",
79056
+ "[9585/10000] (7.78GB) Downloading: nationwidechildrens.org_clinical.TCGA-B6-A2IU.xml (0.05 MB)... "
79057
+ ]
79058
+ },
79059
+ {
79060
+ "name": "stdout",
79061
+ "output_type": "stream",
79062
+ "text": [
79063
+ "OK\n",
79064
+ "[9586/10000] (7.78GB) Downloading: CELLA_p_TCGA_177_179_Esph_SNP_N_GenomeWideSNP_6_D10_871018.nocnv_grch38.seg.v2.txt (0.00 MB)... "
79065
+ ]
79066
+ },
79067
+ {
79068
+ "name": "stdout",
79069
+ "output_type": "stream",
79070
+ "text": [
79071
+ "OK\n",
79072
+ "[9587/10000] (7.78GB) Downloading: 254e6e3e-e30e-46c3-890a-18df11361eac_noid_Red.idat (7.72 MB)... "
79073
+ ]
79074
+ },
79075
+ {
79076
+ "name": "stdout",
79077
+ "output_type": "stream",
79078
+ "text": [
79079
+ "OK\n",
79080
+ "[9588/10000] (7.79GB) Downloading: b37abe51-b52c-4054-ac3b-76d00e62cd1c.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
79081
+ ]
79082
+ },
79083
+ {
79084
+ "name": "stdout",
79085
+ "output_type": "stream",
79086
+ "text": [
79087
+ "OK\n",
79088
+ "[9589/10000] (7.79GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-C8-A12N.xml (0.06 MB)... "
79089
+ ]
79090
+ },
79091
+ {
79092
+ "name": "stdout",
79093
+ "output_type": "stream",
79094
+ "text": [
79095
+ "OK\n",
79096
+ "[9590/10000] (7.79GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_H08_667182.grch38.seg.v2.txt (0.03 MB)... "
79097
+ ]
79098
+ },
79099
+ {
79100
+ "name": "stdout",
79101
+ "output_type": "stream",
79102
+ "text": [
79103
+ "OK\n",
79104
+ "[9591/10000] (7.79GB) Downloading: TCGA-AQ-A04J-01A-02-MS2.e47ffa6a-8d29-4a72-885f-be1d984b00c7.svs (448.74 MB)... "
79105
+ ]
79106
+ },
79107
+ {
79108
+ "name": "stdout",
79109
+ "output_type": "stream",
79110
+ "text": [
79111
+ "OK\n",
79112
+ "[9592/10000] (8.23GB) Downloading: TCGA-C8-A12N.A845013D-BF15-42FB-8BFE-FCE206E943FE.PDF (0.44 MB)... "
79113
+ ]
79114
+ },
79115
+ {
79116
+ "name": "stdout",
79117
+ "output_type": "stream",
79118
+ "text": [
79119
+ "OK\n",
79120
+ "[9593/10000] (8.23GB) Downloading: TCGA-AQ-A04J-01A-02D-A89H-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.09 MB)... "
79121
+ ]
79122
+ },
79123
+ {
79124
+ "name": "stdout",
79125
+ "output_type": "stream",
79126
+ "text": [
79127
+ "OK\n",
79128
+ "[9594/10000] (8.23GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_D04_747896.nocnv_grch38.seg.v2.txt (0.00 MB)... "
79129
+ ]
79130
+ },
79131
+ {
79132
+ "name": "stdout",
79133
+ "output_type": "stream",
79134
+ "text": [
79135
+ "OK\n",
79136
+ "[9595/10000] (8.23GB) Downloading: nationwidechildrens.org_clinical.TCGA-AQ-A04J.xml (0.08 MB)... "
79137
+ ]
79138
+ },
79139
+ {
79140
+ "name": "stdout",
79141
+ "output_type": "stream",
79142
+ "text": [
79143
+ "OK\n",
79144
+ "[9596/10000] (8.23GB) Downloading: TCGA-BRCA.ffbdf887-0c9a-40c0-971a-61eb2bb70e2a.ascat3.allelic_specific.seg.txt (0.01 MB)... "
79145
+ ]
79146
+ },
79147
+ {
79148
+ "name": "stdout",
79149
+ "output_type": "stream",
79150
+ "text": [
79151
+ "OK\n",
79152
+ "[9597/10000] (8.23GB) Downloading: 7647345c-1654-490f-9a18-b43005225bce.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
79153
+ ]
79154
+ },
79155
+ {
79156
+ "name": "stdout",
79157
+ "output_type": "stream",
79158
+ "text": [
79159
+ "OK\n",
79160
+ "[9598/10000] (8.23GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_C01_667192.nocnv_grch38.seg.v2.txt (0.02 MB)... "
79161
+ ]
79162
+ },
79163
+ {
79164
+ "name": "stdout",
79165
+ "output_type": "stream",
79166
+ "text": [
79167
+ "OK\n",
79168
+ "[9599/10000] (8.23GB) Downloading: TCGA-C8-A12N-01A-21-A13D-20_RPPA_data.tsv (0.02 MB)... "
79169
+ ]
79170
+ },
79171
+ {
79172
+ "name": "stdout",
79173
+ "output_type": "stream",
79174
+ "text": [
79175
+ "OK\n",
79176
+ "[9600/10000] (8.23GB) Downloading: TCGA-BRCA.57b92480-0f4d-436d-b6f0-1d01a2d6ce21.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
79177
+ ]
79178
+ },
79179
+ {
79180
+ "name": "stdout",
79181
+ "output_type": "stream",
79182
+ "text": [
79183
+ "OK\n",
79184
+ "[9601/10000] (8.24GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_E09_735356.nocnv_grch38.seg.v2.txt (0.00 MB)... "
79185
+ ]
79186
+ },
79187
+ {
79188
+ "name": "stdout",
79189
+ "output_type": "stream",
79190
+ "text": [
79191
+ "OK\n",
79192
+ "[9602/10000] (8.24GB) Downloading: TCGA-AQ-A04J.71CEC5F6-16E5-46E1-A91B-B5E0F699B231.PDF (0.24 MB)... "
79193
+ ]
79194
+ },
79195
+ {
79196
+ "name": "stdout",
79197
+ "output_type": "stream",
79198
+ "text": [
79199
+ "OK\n",
79200
+ "[9603/10000] (8.24GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_F10_735296.nocnv_grch38.seg.v2.txt (0.00 MB)... "
79201
+ ]
79202
+ },
79203
+ {
79204
+ "name": "stdout",
79205
+ "output_type": "stream",
79206
+ "text": [
79207
+ "OK\n",
79208
+ "[9604/10000] (8.24GB) Downloading: TCGA-BRCA.57b92480-0f4d-436d-b6f0-1d01a2d6ce21.ascat2.allelic_specific.seg.txt (0.01 MB)... "
79209
+ ]
79210
+ },
79211
+ {
79212
+ "name": "stdout",
79213
+ "output_type": "stream",
79214
+ "text": [
79215
+ "OK\n",
79216
+ "[9605/10000] (8.24GB) Downloading: TCGA-AR-A1AQ.FC236604-AAE5-4394-9D39-270FFEFB635A.PDF (0.05 MB)... "
79217
+ ]
79218
+ },
79219
+ {
79220
+ "name": "stdout",
79221
+ "output_type": "stream",
79222
+ "text": [
79223
+ "OK\n",
79224
+ "[9606/10000] (8.24GB) Downloading: a5b2eb51-c105-4612-9391-cfc9ff39b3b2_noid_Grn.idat (0.69 MB)... "
79225
+ ]
79226
+ },
79227
+ {
79228
+ "name": "stdout",
79229
+ "output_type": "stream",
79230
+ "text": [
79231
+ "OK\n",
79232
+ "[9607/10000] (8.24GB) Downloading: TCGA-BRCA.ffbdf887-0c9a-40c0-971a-61eb2bb70e2a.gene_level_copy_number.v36.tsv (3.29 MB)... "
79233
+ ]
79234
+ },
79235
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79238
+ "text": [
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+ "OK\n",
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+ "[9608/10000] (8.24GB) Downloading: nationwidechildrens.org_ssf.TCGA-AQ-A04J.xml (0.01 MB)... "
79241
+ ]
79242
+ },
79243
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79246
+ "text": [
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+ "OK\n",
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+ "[9609/10000] (8.24GB) Downloading: TCGA-BRCA.48becee8-1c71-4320-b0e8-72e345797daf.ascat3.allelic_specific.seg.txt (0.00 MB)... "
79249
+ ]
79250
+ },
79251
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79254
+ "text": [
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+ "OK\n",
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+ "[9610/10000] (8.24GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-LL-A5YO.xml (0.05 MB)... "
79257
+ ]
79258
+ },
79259
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79262
+ "text": [
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+ "OK\n",
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+ "[9611/10000] (8.24GB) Downloading: e9767d1c-cfad-4a5d-92e8-4d963225d233.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
79265
+ ]
79266
+ },
79267
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79270
+ "text": [
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+ "OK\n",
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+ "[9612/10000] (8.24GB) Downloading: TCGA-BRCA.51c263b0-32eb-49fe-b7ed-7de6b0a94c33.gene_level_copy_number.v36.tsv (3.29 MB)... "
79273
+ ]
79274
+ },
79275
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79278
+ "text": [
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+ "OK\n",
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+ "[9613/10000] (8.24GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AQ-A04J.xml (0.09 MB)... "
79281
+ ]
79282
+ },
79283
+ {
79284
+ "name": "stdout",
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+ "output_type": "stream",
79286
+ "text": [
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+ "OK\n",
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+ "[9614/10000] (8.25GB) Downloading: 8fcab2a8-6ac5-4236-a774-0239676de66d_noid_Red.idat (7.72 MB)... "
79289
+ ]
79290
+ },
79291
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79294
+ "text": [
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+ "OK\n",
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+ "[9615/10000] (8.25GB) Downloading: TCGA-LL-A5YO-01A-21D-A89E-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.04 MB)... "
79297
+ ]
79298
+ },
79299
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79302
+ "text": [
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+ "OK\n",
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+ "[9616/10000] (8.25GB) Downloading: DRIPS_p_TCGA_295_296_297_N_GenomeWideSNP_6_H06_1343768.grch38.seg.v2.txt (0.02 MB)... "
79305
+ ]
79306
+ },
79307
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79310
+ "text": [
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+ "OK\n",
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+ "[9617/10000] (8.25GB) Downloading: 8fcab2a8-6ac5-4236-a774-0239676de66d.methylation_array.sesame.level3betas.txt (12.53 MB)... "
79313
+ ]
79314
+ },
79315
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79318
+ "text": [
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+ "OK\n",
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+ "[9618/10000] (8.26GB) Downloading: TCGA-E9-A1N9.39D6D1DE-2CAE-470F-836B-926242F46E67.PDF (0.05 MB)... "
79321
+ ]
79322
+ },
79323
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79326
+ "text": [
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+ "OK\n",
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+ "[9619/10000] (8.26GB) Downloading: 9d107405-9901-41ac-b047-90bf2dae7b50.mirbase21.mirnas.quantification.txt (0.05 MB)... "
79329
+ ]
79330
+ },
79331
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79334
+ "text": [
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+ "OK\n",
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+ "[9620/10000] (8.26GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_F01_1373640.nocnv_grch38.seg.v2.txt (0.01 MB)... "
79337
+ ]
79338
+ },
79339
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79342
+ "text": [
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+ "OK\n",
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+ "[9621/10000] (8.26GB) Downloading: TCGA-LL-A5YO-01A-02-TS2.5819C502-EEA4-4D98-B4EC-E184B374ECFB.svs (110.88 MB)... "
79345
+ ]
79346
+ },
79347
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79350
+ "text": [
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+ "OK\n",
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+ "[9622/10000] (8.37GB) Downloading: TCGA-LL-A5YO-01A-11-A321-20_RPPA_data.tsv (0.02 MB)... "
79353
+ ]
79354
+ },
79355
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79358
+ "text": [
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+ "OK\n",
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+ "[9623/10000] (8.37GB) Downloading: TCGA-A7-A6VW-01Z-00-DX1.1BC4790C-DB45-4A3D-9C97-92C92C03FF60.svs (423.58 MB)... "
79361
+ ]
79362
+ },
79363
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79366
+ "text": [
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+ "OK\n",
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+ "[9624/10000] (8.79GB) Downloading: CHEEP_p_TCGA_b120_121_SNP_N_GenomeWideSNP_6_F02_777578.grch38.seg.v2.txt (0.02 MB)... "
79369
+ ]
79370
+ },
79371
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79374
+ "text": [
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+ "OK\n",
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+ "[9625/10000] (8.79GB) Downloading: TCGA-E9-A1N9-01A-21-A17K-20_RPPA_data.tsv (0.02 MB)... "
79377
+ ]
79378
+ },
79379
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79382
+ "text": [
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+ "OK\n",
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+ "[9626/10000] (8.79GB) Downloading: TCGA-A7-A6VW.BE19CEFA-7A66-480C-BEC0-AF52F4C8A04C.PDF (0.09 MB)... "
79385
+ ]
79386
+ },
79387
+ {
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+ "name": "stdout",
79389
+ "output_type": "stream",
79390
+ "text": [
79391
+ "OK\n",
79392
+ "[9627/10000] (8.79GB) Downloading: TCGA-E9-A1N9-01A-11D-A897-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.17 MB)... "
79393
+ ]
79394
+ },
79395
+ {
79396
+ "name": "stdout",
79397
+ "output_type": "stream",
79398
+ "text": [
79399
+ "OK\n",
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+ "[9628/10000] (8.79GB) Downloading: TCGA-E9-A1N9-11A-06-TSF.b5735423-f834-4dc4-839e-5ef558af32c2.svs (38.94 MB)... "
79401
+ ]
79402
+ },
79403
+ {
79404
+ "name": "stdout",
79405
+ "output_type": "stream",
79406
+ "text": [
79407
+ "OK\n",
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+ "[9629/10000] (8.83GB) Downloading: d2a22372-6fd9-4aa6-88b0-7bebb8a156d8.mirbase21.mirnas.quantification.txt (0.05 MB)... "
79409
+ ]
79410
+ },
79411
+ {
79412
+ "name": "stdout",
79413
+ "output_type": "stream",
79414
+ "text": [
79415
+ "OK\n",
79416
+ "[9630/10000] (8.83GB) Downloading: TCGA-A8-A08A.6D2212CE-C80F-4545-A895-3F1B6E4C6DB6.PDF (0.05 MB)... "
79417
+ ]
79418
+ },
79419
+ {
79420
+ "name": "stdout",
79421
+ "output_type": "stream",
79422
+ "text": [
79423
+ "OK\n",
79424
+ "[9631/10000] (8.83GB) Downloading: 42fcc484-0092-4f27-ac5d-61a907fd57c8_noid_Red.idat (7.72 MB)... "
79425
+ ]
79426
+ },
79427
+ {
79428
+ "name": "stdout",
79429
+ "output_type": "stream",
79430
+ "text": [
79431
+ "OK\n",
79432
+ "[9632/10000] (8.83GB) Downloading: TCGA-BRCA.46a7082e-19e7-4f1a-806b-31c2db120c34.ascat3.allelic_specific.seg.txt (0.00 MB)... "
79433
+ ]
79434
+ },
79435
+ {
79436
+ "name": "stdout",
79437
+ "output_type": "stream",
79438
+ "text": [
79439
+ "OK\n",
79440
+ "[9633/10000] (8.83GB) Downloading: f953c835-697b-4758-a98f-829b420fb373.methylation_array.sesame.level3betas.txt (0.74 MB)... "
79441
+ ]
79442
+ },
79443
+ {
79444
+ "name": "stdout",
79445
+ "output_type": "stream",
79446
+ "text": [
79447
+ "OK\n",
79448
+ "[9634/10000] (8.83GB) Downloading: TCGA-BRCA.5ae97b02-7893-4ef8-83aa-585b87983f37.ascat3.allelic_specific.seg.txt (0.02 MB)... "
79449
+ ]
79450
+ },
79451
+ {
79452
+ "name": "stdout",
79453
+ "output_type": "stream",
79454
+ "text": [
79455
+ "OK\n",
79456
+ "[9635/10000] (8.83GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_G10_628232.grch38.seg.v2.txt (0.03 MB)... "
79457
+ ]
79458
+ },
79459
+ {
79460
+ "name": "stdout",
79461
+ "output_type": "stream",
79462
+ "text": [
79463
+ "OK\n",
79464
+ "[9636/10000] (8.83GB) Downloading: 171e095d-2236-43c8-9670-23608e6cc8ab.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
79465
+ ]
79466
+ },
79467
+ {
79468
+ "name": "stdout",
79469
+ "output_type": "stream",
79470
+ "text": [
79471
+ "OK\n",
79472
+ "[9637/10000] (8.84GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A08A.xml (0.03 MB)... "
79473
+ ]
79474
+ },
79475
+ {
79476
+ "name": "stdout",
79477
+ "output_type": "stream",
79478
+ "text": [
79479
+ "OK\n",
79480
+ "[9638/10000] (8.84GB) Downloading: TCGA-BRCA.46a7082e-19e7-4f1a-806b-31c2db120c34.ascat2.allelic_specific.seg.txt (0.01 MB)... "
79481
+ ]
79482
+ },
79483
+ {
79484
+ "name": "stdout",
79485
+ "output_type": "stream",
79486
+ "text": [
79487
+ "OK\n",
79488
+ "[9639/10000] (8.84GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_E03_628254.nocnv_grch38.seg.v2.txt (0.01 MB)... "
79489
+ ]
79490
+ },
79491
+ {
79492
+ "name": "stdout",
79493
+ "output_type": "stream",
79494
+ "text": [
79495
+ "OK\n",
79496
+ "[9640/10000] (8.84GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_G10_628232.nocnv_grch38.seg.v2.txt (0.01 MB)... "
79497
+ ]
79498
+ },
79499
+ {
79500
+ "name": "stdout",
79501
+ "output_type": "stream",
79502
+ "text": [
79503
+ "OK\n",
79504
+ "[9641/10000] (8.84GB) Downloading: 9b413ca5-5a75-4ceb-9059-0f772af2fbe5.mirbase21.isoforms.quantification.txt (0.18 MB)... "
79505
+ ]
79506
+ },
79507
+ {
79508
+ "name": "stdout",
79509
+ "output_type": "stream",
79510
+ "text": [
79511
+ "OK\n",
79512
+ "[9642/10000] (8.84GB) Downloading: 3cbdea8d-8a71-4fe6-b605-b196e3abe55f.mirbase21.mirnas.quantification.txt (0.05 MB)... "
79513
+ ]
79514
+ },
79515
+ {
79516
+ "name": "stdout",
79517
+ "output_type": "stream",
79518
+ "text": [
79519
+ "OK\n",
79520
+ "[9643/10000] (8.84GB) Downloading: TCGA-A8-A08A-01Z-00-DX1.3BB777A0-8652-4483-8DD6-8EB88AB0A8EF.svs (594.47 MB)... "
79521
+ ]
79522
+ },
79523
+ {
79524
+ "name": "stdout",
79525
+ "output_type": "stream",
79526
+ "text": [
79527
+ "OK\n",
79528
+ "[9644/10000] (9.42GB) Downloading: TCGA-A8-A08A-01A-01-TS1.e7bdf564-67d2-46dc-bd6a-439cdc74e163.svs (306.94 MB)... "
79529
+ ]
79530
+ },
79531
+ {
79532
+ "name": "stdout",
79533
+ "output_type": "stream",
79534
+ "text": [
79535
+ "OK\n",
79536
+ "[9645/10000] (9.72GB) Downloading: d2a22372-6fd9-4aa6-88b0-7bebb8a156d8.mirbase21.isoforms.quantification.txt (0.24 MB)... "
79537
+ ]
79538
+ },
79539
+ {
79540
+ "name": "stdout",
79541
+ "output_type": "stream",
79542
+ "text": [
79543
+ "OK\n",
79544
+ "[9646/10000] (9.72GB) Downloading: TCGA-A8-A08A-01A-21-A13A-20_RPPA_data.tsv (0.02 MB)... "
79545
+ ]
79546
+ },
79547
+ {
79548
+ "name": "stdout",
79549
+ "output_type": "stream",
79550
+ "text": [
79551
+ "OK\n",
79552
+ "[9647/10000] (9.72GB) Downloading: 0631de29-6e9a-4928-ab8a-c76bd44dbd45.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
79553
+ ]
79554
+ },
79555
+ {
79556
+ "name": "stdout",
79557
+ "output_type": "stream",
79558
+ "text": [
79559
+ "OK\n",
79560
+ "[9648/10000] (9.72GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-D8-A4Z1.xml (0.05 MB)... "
79561
+ ]
79562
+ },
79563
+ {
79564
+ "name": "stdout",
79565
+ "output_type": "stream",
79566
+ "text": [
79567
+ "OK\n",
79568
+ "[9649/10000] (9.72GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_C06_1320422.nocnv_grch38.seg.v2.txt (0.00 MB)... "
79569
+ ]
79570
+ },
79571
+ {
79572
+ "name": "stdout",
79573
+ "output_type": "stream",
79574
+ "text": [
79575
+ "OK\n",
79576
+ "[9650/10000] (9.72GB) Downloading: TCGA-E9-A1N9-01A-01-TSA.dec56c61-13f3-4eda-898b-1f2e40b6f54a.svs (227.02 MB)... "
79577
+ ]
79578
+ },
79579
+ {
79580
+ "name": "stdout",
79581
+ "output_type": "stream",
79582
+ "text": [
79583
+ "OK\n",
79584
+ "[9651/10000] (9.94GB) Downloading: nationwidechildrens.org_ssf.TCGA-E9-A1N9.xml (0.02 MB)... "
79585
+ ]
79586
+ },
79587
+ {
79588
+ "name": "stdout",
79589
+ "output_type": "stream",
79590
+ "text": [
79591
+ "OK\n",
79592
+ "[9652/10000] (9.94GB) Downloading: nationwidechildrens.org_clinical.TCGA-D8-A4Z1.xml (0.06 MB)... "
79593
+ ]
79594
+ },
79595
+ {
79596
+ "name": "stdout",
79597
+ "output_type": "stream",
79598
+ "text": [
79599
+ "OK\n",
79600
+ "[9653/10000] (9.94GB) Downloading: d8cc13a3-f04b-4353-9da0-db1549244346.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
79601
+ ]
79602
+ },
79603
+ {
79604
+ "name": "stdout",
79605
+ "output_type": "stream",
79606
+ "text": [
79607
+ "OK\n",
79608
+ "[9654/10000] (9.94GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A0A7.xml (0.09 MB)... "
79609
+ ]
79610
+ },
79611
+ {
79612
+ "name": "stdout",
79613
+ "output_type": "stream",
79614
+ "text": [
79615
+ "OK\n",
79616
+ "[9655/10000] (9.94GB) Downloading: b3512896-94fe-489d-bd88-9d0858857bd0.wxs.aliquot_ensemble_masked.maf.gz (0.08 MB)... "
79617
+ ]
79618
+ },
79619
+ {
79620
+ "name": "stdout",
79621
+ "output_type": "stream",
79622
+ "text": [
79623
+ "OK\n",
79624
+ "[9656/10000] (9.94GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_D02_628476.nocnv_grch38.seg.v2.txt (0.01 MB)... "
79625
+ ]
79626
+ },
79627
+ {
79628
+ "name": "stdout",
79629
+ "output_type": "stream",
79630
+ "text": [
79631
+ "OK\n",
79632
+ "[9657/10000] (9.94GB) Downloading: a75296ed-0a6a-45aa-9483-e550417976ce_noid_Red.idat (7.72 MB)... "
79633
+ ]
79634
+ },
79635
+ {
79636
+ "name": "stdout",
79637
+ "output_type": "stream",
79638
+ "text": [
79639
+ "OK\n",
79640
+ "[9658/10000] (9.95GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_C10_1320354.grch38.seg.v2.txt (0.03 MB)... "
79641
+ ]
79642
+ },
79643
+ {
79644
+ "name": "stdout",
79645
+ "output_type": "stream",
79646
+ "text": [
79647
+ "OK\n",
79648
+ "[9659/10000] (9.95GB) Downloading: TCGA-A8-A0A7.E306BE26-0358-4BE4-AEF6-AD42CC0DA020.PDF (0.09 MB)... "
79649
+ ]
79650
+ },
79651
+ {
79652
+ "name": "stdout",
79653
+ "output_type": "stream",
79654
+ "text": [
79655
+ "OK\n",
79656
+ "[9660/10000] (9.95GB) Downloading: TCGA-D8-A4Z1-01Z-00-DX1.D39D38B5-FC9F-4298-8720-016407DC6591.svs (990.22 MB)... "
79657
+ ]
79658
+ },
79659
+ {
79660
+ "name": "stdout",
79661
+ "output_type": "stream",
79662
+ "text": [
79663
+ "OK\n",
79664
+ "[9661/10000] (10.92GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_C06_1320422.grch38.seg.v2.txt (0.02 MB)... "
79665
+ ]
79666
+ },
79667
+ {
79668
+ "name": "stdout",
79669
+ "output_type": "stream",
79670
+ "text": [
79671
+ "OK\n",
79672
+ "[9662/10000] (10.92GB) Downloading: TCGA-BRCA.f552a80d-3e4c-4c0b-b827-806305e48a35.gene_level_copy_number.v36.tsv (3.29 MB)... "
79673
+ ]
79674
+ },
79675
+ {
79676
+ "name": "stdout",
79677
+ "output_type": "stream",
79678
+ "text": [
79679
+ "OK\n",
79680
+ "[9663/10000] (10.92GB) Downloading: nationwidechildrens.org_ssf.TCGA-D8-A4Z1.xml (0.01 MB)... "
79681
+ ]
79682
+ },
79683
+ {
79684
+ "name": "stdout",
79685
+ "output_type": "stream",
79686
+ "text": [
79687
+ "OK\n",
79688
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+ },
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+ {
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+ "name": "stdout",
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+ "text": [
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9667/10000] (10.92GB) Downloading: TCGA-D8-A4Z1-01A-02-TS2.8713DF53-D04B-41D2-B9BB-3B1D31B1738E.svs (192.33 MB)... "
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9668/10000] (11.11GB) Downloading: 0007e90d-3186-4967-905c-22aa24049d44.methylation_array.sesame.level3betas.txt (0.73 MB)... "
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9669/10000] (11.11GB) Downloading: TCGA-BRCA.f552a80d-3e4c-4c0b-b827-806305e48a35.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9670/10000] (11.11GB) Downloading: f00dddc4-9a26-4569-aa6f-c6f65341283a.mirbase21.mirnas.quantification.txt (0.05 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9671/10000] (11.11GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_C11_628504.nocnv_grch38.seg.v2.txt (0.00 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9672/10000] (11.11GB) Downloading: TCGA-EW-A1P0-01A-21-A17J-20_RPPA_data.tsv (0.02 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9673/10000] (11.11GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_E05_778034.nocnv_grch38.seg.v2.txt (0.01 MB)... "
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+ ]
79762
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9674/10000] (11.11GB) Downloading: TCGA-BRCA.0d7cde44-ec86-415a-8667-0ea894d1c344.gene_level_copy_number.v36.tsv (3.29 MB)... "
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+ ]
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+ },
79771
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9675/10000] (11.12GB) Downloading: TCGA-A2-A1FZ-01A-05-TSE.92edfd43-6c1e-4b2c-851e-e0968ad67036.svs (124.18 MB)... "
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+ },
79779
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9676/10000] (11.24GB) Downloading: TCGA-BRCA.c5e3d0a9-e703-4c1c-92eb-3dcc093d14e2.ascat3.allelic_specific.seg.txt (0.01 MB)... "
79785
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9677/10000] (11.24GB) Downloading: 82279cae-423a-487b-89b8-069dbd28c3a1_noid_Red.idat (0.69 MB)... "
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+ ]
79794
+ },
79795
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9678/10000] (11.24GB) Downloading: nationwidechildrens.org_clinical.TCGA-AO-A1KR.xml (0.07 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9679/10000] (11.24GB) Downloading: TCGA-BRCA.2324a415-fc47-477f-8842-822a48b120a6.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
79809
+ ]
79810
+ },
79811
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9680/10000] (11.24GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_D04_778116.nocnv_grch38.seg.v2.txt (0.04 MB)... "
79817
+ ]
79818
+ },
79819
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9681/10000] (11.24GB) Downloading: TCGA-BRCA.0d7cde44-ec86-415a-8667-0ea894d1c344.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
79825
+ ]
79826
+ },
79827
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79830
+ "text": [
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+ "OK\n",
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+ "[9682/10000] (11.25GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_F04_778026.nocnv_grch38.seg.v2.txt (0.00 MB)... "
79833
+ ]
79834
+ },
79835
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9683/10000] (11.25GB) Downloading: fbeb9131-20a7-4cd8-a1ac-d3a1aaef1c1b.wxs.aliquot_ensemble_masked.maf.gz (0.03 MB)... "
79841
+ ]
79842
+ },
79843
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79846
+ "text": [
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+ "OK\n",
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+ "[9684/10000] (11.25GB) Downloading: 6cbd5498-f78e-499d-9428-df4577d4dcd2_noid_Grn.idat (7.72 MB)... "
79849
+ ]
79850
+ },
79851
+ {
79852
+ "name": "stdout",
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+ "output_type": "stream",
79854
+ "text": [
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+ "OK\n",
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+ "[9685/10000] (11.25GB) Downloading: TCGA-AO-A1KR-01A-01-TSA.78fa04a1-d5f6-4468-9da5-72e7abb8de86.svs (234.94 MB)... "
79857
+ ]
79858
+ },
79859
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79862
+ "text": [
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+ "OK\n",
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+ "[9686/10000] (11.48GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A09Z.xml (0.09 MB)... "
79865
+ ]
79866
+ },
79867
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9687/10000] (11.48GB) Downloading: d95551e6-8263-4fd9-9fc2-9a4070739277.methylation_array.sesame.level3betas.txt (12.58 MB)... "
79873
+ ]
79874
+ },
79875
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
79878
+ "text": [
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+ "OK\n",
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+ "[9688/10000] (11.50GB) Downloading: TCGA-BRCA.2324a415-fc47-477f-8842-822a48b120a6.ascat3.allelic_specific.seg.txt (0.00 MB)... "
79881
+ ]
79882
+ },
79883
+ {
79884
+ "name": "stdout",
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+ "output_type": "stream",
79886
+ "text": [
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+ "OK\n",
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+ "[9689/10000] (11.50GB) Downloading: TCGA-A2-A1FZ-01Z-00-DX1.0BAAEF41-DCA4-4677-9A27-09E990033FA6.svs (922.48 MB)... "
79889
+ ]
79890
+ },
79891
+ {
79892
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9690/10000] (12.40GB) Downloading: 6cbd5498-f78e-499d-9428-df4577d4dcd2.methylation_array.sesame.level3betas.txt (12.52 MB)... "
79897
+ ]
79898
+ },
79899
+ {
79900
+ "name": "stdout",
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+ "output_type": "stream",
79902
+ "text": [
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+ "OK\n",
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+ "[9691/10000] (12.41GB) Downloading: 6341abdb-a59a-4c58-97f2-cc9bcfef1b8d_noid_Red.idat (7.72 MB)... "
79905
+ ]
79906
+ },
79907
+ {
79908
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9692/10000] (12.42GB) Downloading: d95551e6-8263-4fd9-9fc2-9a4070739277_noid_Grn.idat (7.72 MB)... "
79913
+ ]
79914
+ },
79915
+ {
79916
+ "name": "stdout",
79917
+ "output_type": "stream",
79918
+ "text": [
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+ "OK\n",
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+ "[9693/10000] (12.42GB) Downloading: TCGA-BRCA.0d7cde44-ec86-415a-8667-0ea894d1c344.ascat3.allelic_specific.seg.txt (0.01 MB)... "
79921
+ ]
79922
+ },
79923
+ {
79924
+ "name": "stdout",
79925
+ "output_type": "stream",
79926
+ "text": [
79927
+ "OK\n",
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+ "[9694/10000] (12.42GB) Downloading: TCGA-AO-A1KR.FF188295-E139-4AEE-8EE8-364536F2BBE8.PDF (0.17 MB)... "
79929
+ ]
79930
+ },
79931
+ {
79932
+ "name": "stdout",
79933
+ "output_type": "stream",
79934
+ "text": [
79935
+ "OK\n",
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+ "[9695/10000] (12.42GB) Downloading: TCGA-A8-A09Z-01A-21-A13A-20_RPPA_data.tsv (0.02 MB)... "
79937
+ ]
79938
+ },
79939
+ {
79940
+ "name": "stdout",
79941
+ "output_type": "stream",
79942
+ "text": [
79943
+ "OK\n",
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+ "[9696/10000] (12.42GB) Downloading: b1d64529-4f34-4644-b0e7-20606827ccd4.rna_seq.augmented_star_gene_counts.tsv (4.03 MB)... "
79945
+ ]
79946
+ },
79947
+ {
79948
+ "name": "stdout",
79949
+ "output_type": "stream",
79950
+ "text": [
79951
+ "OK\n",
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+ "[9697/10000] (12.43GB) Downloading: 6341abdb-a59a-4c58-97f2-cc9bcfef1b8d.methylation_array.sesame.level3betas.txt (12.45 MB)... "
79953
+ ]
79954
+ },
79955
+ {
79956
+ "name": "stdout",
79957
+ "output_type": "stream",
79958
+ "text": [
79959
+ "OK\n",
79960
+ "[9698/10000] (12.44GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E9-A3HO.xml (0.05 MB)... "
79961
+ ]
79962
+ },
79963
+ {
79964
+ "name": "stdout",
79965
+ "output_type": "stream",
79966
+ "text": [
79967
+ "OK\n",
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+ "[9699/10000] (12.44GB) Downloading: MINAE_p_TCGA_200_202_203_SNP_N_GenomeWideSNP_6_G05_955136.nocnv_grch38.seg.v2.txt (0.02 MB)... "
79969
+ ]
79970
+ },
79971
+ {
79972
+ "name": "stdout",
79973
+ "output_type": "stream",
79974
+ "text": [
79975
+ "OK\n",
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+ "[9700/10000] (12.44GB) Downloading: ce7471cc-a727-42bb-bded-e4a657e5b8fb.mirbase21.mirnas.quantification.txt (0.05 MB)... "
79977
+ ]
79978
+ },
79979
+ {
79980
+ "name": "stdout",
79981
+ "output_type": "stream",
79982
+ "text": [
79983
+ "OK\n",
79984
+ "[9701/10000] (12.44GB) Downloading: TCGA-E9-A3HO.3EFA8B1E-0FDB-49A4-95FC-4C9C9B15B61A.PDF (0.08 MB)... "
79985
+ ]
79986
+ },
79987
+ {
79988
+ "name": "stdout",
79989
+ "output_type": "stream",
79990
+ "text": [
79991
+ "OK\n",
79992
+ "[9702/10000] (12.44GB) Downloading: TCGA-BRCA.b451d230-d158-40cb-91a9-bf25a4da50e6.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
79993
+ ]
79994
+ },
79995
+ {
79996
+ "name": "stdout",
79997
+ "output_type": "stream",
79998
+ "text": [
79999
+ "OK\n",
80000
+ "[9703/10000] (12.44GB) Downloading: TCGA-E9-A3HO-01A-21-A24A-20_RPPA_data.tsv (0.02 MB)... "
80001
+ ]
80002
+ },
80003
+ {
80004
+ "name": "stdout",
80005
+ "output_type": "stream",
80006
+ "text": [
80007
+ "OK\n",
80008
+ "[9704/10000] (12.44GB) Downloading: TCGA-OL-A5RU-01Z-00-DX1.A48CAF2D-9310-4611-B27D-400F3A324607.svs (53.74 MB)... "
80009
+ ]
80010
+ },
80011
+ {
80012
+ "name": "stdout",
80013
+ "output_type": "stream",
80014
+ "text": [
80015
+ "OK\n",
80016
+ "[9705/10000] (12.50GB) Downloading: TCGA-E2-A10B-01A-01-TS1.3bfc66da-c6c4-4246-8794-4b477deba098.svs (518.08 MB)... "
80017
+ ]
80018
+ },
80019
+ {
80020
+ "name": "stdout",
80021
+ "output_type": "stream",
80022
+ "text": [
80023
+ "OK\n",
80024
+ "[9706/10000] (13.00GB) Downloading: nationwidechildrens.org_ssf.TCGA-E9-A3HO.xml (0.01 MB)... "
80025
+ ]
80026
+ },
80027
+ {
80028
+ "name": "stdout",
80029
+ "output_type": "stream",
80030
+ "text": [
80031
+ "OK\n",
80032
+ "[9707/10000] (13.00GB) Downloading: TCGA-E2-A10B-01A-11D-A894-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.13 MB)... "
80033
+ ]
80034
+ },
80035
+ {
80036
+ "name": "stdout",
80037
+ "output_type": "stream",
80038
+ "text": [
80039
+ "OK\n",
80040
+ "[9708/10000] (13.00GB) Downloading: nationwidechildrens.org_clinical.TCGA-E2-A10B.xml (0.09 MB)... "
80041
+ ]
80042
+ },
80043
+ {
80044
+ "name": "stdout",
80045
+ "output_type": "stream",
80046
+ "text": [
80047
+ "OK\n",
80048
+ "[9709/10000] (13.00GB) Downloading: TCGA-OL-A5RU.7507AC79-4C8E-4393-92B9-BFA6BEB492D0.PDF (1.18 MB)... "
80049
+ ]
80050
+ },
80051
+ {
80052
+ "name": "stdout",
80053
+ "output_type": "stream",
80054
+ "text": [
80055
+ "OK\n",
80056
+ "[9710/10000] (13.00GB) Downloading: TCGA-E9-A3HO-01Z-00-DX1.8C897764-4CD4-40DE-9F8B-7F1BE5FF89C7.svs (832.65 MB)... "
80057
+ ]
80058
+ },
80059
+ {
80060
+ "name": "stdout",
80061
+ "output_type": "stream",
80062
+ "text": [
80063
+ "OK\n",
80064
+ "[9711/10000] (13.82GB) Downloading: MINAE_p_TCGA_200_202_203_SNP_N_GenomeWideSNP_6_D07_955144.nocnv_grch38.seg.v2.txt (0.00 MB)... "
80065
+ ]
80066
+ },
80067
+ {
80068
+ "name": "stdout",
80069
+ "output_type": "stream",
80070
+ "text": [
80071
+ "OK\n",
80072
+ "[9712/10000] (13.82GB) Downloading: TCGA-BRCA.ce888acf-cb20-43f6-936b-be22ed0f817e.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
80073
+ ]
80074
+ },
80075
+ {
80076
+ "name": "stdout",
80077
+ "output_type": "stream",
80078
+ "text": [
80079
+ "OK\n",
80080
+ "[9713/10000] (13.82GB) Downloading: a5096e4d-945e-42d6-a542-394cdca74458.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
80081
+ ]
80082
+ },
80083
+ {
80084
+ "name": "stdout",
80085
+ "output_type": "stream",
80086
+ "text": [
80087
+ "OK\n",
80088
+ "[9714/10000] (13.82GB) Downloading: TCGA-BRCA.fbdb3e72-fa98-48f6-be78-a112b93de1d4.absolute_liftover.gene_level_copy_number.v36.tsv (3.28 MB)... "
80089
+ ]
80090
+ },
80091
+ {
80092
+ "name": "stdout",
80093
+ "output_type": "stream",
80094
+ "text": [
80095
+ "OK\n",
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+ "[9715/10000] (13.82GB) Downloading: 0b59b278-d2f6-4aa6-bf6d-b8d743ae83af.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
80097
+ ]
80098
+ },
80099
+ {
80100
+ "name": "stdout",
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+ "output_type": "stream",
80102
+ "text": [
80103
+ "OK\n",
80104
+ "[9716/10000] (13.83GB) Downloading: c907ec06-97dc-49c2-996c-d294261951df.mirbase21.mirnas.quantification.txt (0.05 MB)... "
80105
+ ]
80106
+ },
80107
+ {
80108
+ "name": "stdout",
80109
+ "output_type": "stream",
80110
+ "text": [
80111
+ "OK\n",
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+ "[9717/10000] (13.83GB) Downloading: TCGA-BRCA.fd183f1b-305a-48f9-a42b-a0d2711bcadb.gene_level_copy_number.v36.tsv (3.29 MB)... "
80113
+ ]
80114
+ },
80115
+ {
80116
+ "name": "stdout",
80117
+ "output_type": "stream",
80118
+ "text": [
80119
+ "OK\n",
80120
+ "[9718/10000] (13.83GB) Downloading: 78cac381-4aa6-4b8b-88ec-a80905fcd93c_noid_Grn.idat (7.72 MB)... "
80121
+ ]
80122
+ },
80123
+ {
80124
+ "name": "stdout",
80125
+ "output_type": "stream",
80126
+ "text": [
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+ "OK\n",
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+ "[9719/10000] (13.84GB) Downloading: TCGA-BRCA.fd183f1b-305a-48f9-a42b-a0d2711bcadb.absolute_liftover.gene_level_copy_number.v36.tsv (3.28 MB)... "
80129
+ ]
80130
+ },
80131
+ {
80132
+ "name": "stdout",
80133
+ "output_type": "stream",
80134
+ "text": [
80135
+ "OK\n",
80136
+ "[9720/10000] (13.84GB) Downloading: nationwidechildrens.org_clinical.TCGA-OL-A66P.xml (0.07 MB)... "
80137
+ ]
80138
+ },
80139
+ {
80140
+ "name": "stdout",
80141
+ "output_type": "stream",
80142
+ "text": [
80143
+ "OK\n",
80144
+ "[9721/10000] (13.84GB) Downloading: a32190c5-a193-4e90-ac98-38a600bb10f0.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
80145
+ ]
80146
+ },
80147
+ {
80148
+ "name": "stdout",
80149
+ "output_type": "stream",
80150
+ "text": [
80151
+ "OK\n",
80152
+ "[9722/10000] (13.84GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_D03_1373654.grch38.seg.v2.txt (0.02 MB)... "
80153
+ ]
80154
+ },
80155
+ {
80156
+ "name": "stdout",
80157
+ "output_type": "stream",
80158
+ "text": [
80159
+ "OK\n",
80160
+ "[9723/10000] (13.84GB) Downloading: nationwidechildrens.org_omf.TCGA-OL-A5RU.xml (0.01 MB)... "
80161
+ ]
80162
+ },
80163
+ {
80164
+ "name": "stdout",
80165
+ "output_type": "stream",
80166
+ "text": [
80167
+ "OK\n",
80168
+ "[9724/10000] (13.84GB) Downloading: TCGA-OL-A66P.979468F0-6B4A-4759-9CA2-7BA1D1441BC2.PDF (0.36 MB)... "
80169
+ ]
80170
+ },
80171
+ {
80172
+ "name": "stdout",
80173
+ "output_type": "stream",
80174
+ "text": [
80175
+ "OK\n",
80176
+ "[9725/10000] (13.84GB) Downloading: TCGA-BRCA.fd183f1b-305a-48f9-a42b-a0d2711bcadb.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
80177
+ ]
80178
+ },
80179
+ {
80180
+ "name": "stdout",
80181
+ "output_type": "stream",
80182
+ "text": [
80183
+ "OK\n",
80184
+ "[9726/10000] (13.85GB) Downloading: aafcd591-7756-4621-bc0f-d73a449d7bab_noid_Red.idat (7.72 MB)... "
80185
+ ]
80186
+ },
80187
+ {
80188
+ "name": "stdout",
80189
+ "output_type": "stream",
80190
+ "text": [
80191
+ "OK\n",
80192
+ "[9727/10000] (13.86GB) Downloading: addaf3a8-26ce-45e8-b8b1-885f22e567a7.mirbase21.isoforms.quantification.txt (0.28 MB)... "
80193
+ ]
80194
+ },
80195
+ {
80196
+ "name": "stdout",
80197
+ "output_type": "stream",
80198
+ "text": [
80199
+ "OK\n",
80200
+ "[9728/10000] (13.86GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AC-A6IW.xml (0.05 MB)... "
80201
+ ]
80202
+ },
80203
+ {
80204
+ "name": "stdout",
80205
+ "output_type": "stream",
80206
+ "text": [
80207
+ "OK\n",
80208
+ "[9729/10000] (13.86GB) Downloading: aafcd591-7756-4621-bc0f-d73a449d7bab_noid_Grn.idat (7.72 MB)... "
80209
+ ]
80210
+ },
80211
+ {
80212
+ "name": "stdout",
80213
+ "output_type": "stream",
80214
+ "text": [
80215
+ "OK\n",
80216
+ "[9730/10000] (13.86GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_D02_1373598.grch38.seg.v2.txt (0.06 MB)... "
80217
+ ]
80218
+ },
80219
+ {
80220
+ "name": "stdout",
80221
+ "output_type": "stream",
80222
+ "text": [
80223
+ "OK\n",
80224
+ "[9731/10000] (13.86GB) Downloading: TCGA-OL-A66P-01A-21-A321-20_RPPA_data.tsv (0.02 MB)... "
80225
+ ]
80226
+ },
80227
+ {
80228
+ "name": "stdout",
80229
+ "output_type": "stream",
80230
+ "text": [
80231
+ "OK\n",
80232
+ "[9732/10000] (13.86GB) Downloading: f6383414-be87-464a-8859-e98b5c676040.methylation_array.sesame.level3betas.txt (12.49 MB)... "
80233
+ ]
80234
+ },
80235
+ {
80236
+ "name": "stdout",
80237
+ "output_type": "stream",
80238
+ "text": [
80239
+ "OK\n",
80240
+ "[9733/10000] (13.88GB) Downloading: TCGA-AC-A6IW.302E69E0-39F0-4CDB-97F9-A6CDDB3D7233.PDF (0.39 MB)... "
80241
+ ]
80242
+ },
80243
+ {
80244
+ "name": "stdout",
80245
+ "output_type": "stream",
80246
+ "text": [
80247
+ "OK\n",
80248
+ "[9734/10000] (13.88GB) Downloading: f6383414-be87-464a-8859-e98b5c676040_noid_Grn.idat (7.72 MB)... "
80249
+ ]
80250
+ },
80251
+ {
80252
+ "name": "stdout",
80253
+ "output_type": "stream",
80254
+ "text": [
80255
+ "OK\n",
80256
+ "[9735/10000] (13.88GB) Downloading: nationwidechildrens.org_ssf.TCGA-OL-A66P.xml (0.01 MB)... "
80257
+ ]
80258
+ },
80259
+ {
80260
+ "name": "stdout",
80261
+ "output_type": "stream",
80262
+ "text": [
80263
+ "OK\n",
80264
+ "[9736/10000] (13.88GB) Downloading: 0b2aa006-2958-431c-917a-0d9b0c381f66.methylation_array.sesame.level3betas.txt (12.56 MB)... "
80265
+ ]
80266
+ },
80267
+ {
80268
+ "name": "stdout",
80269
+ "output_type": "stream",
80270
+ "text": [
80271
+ "OK\n",
80272
+ "[9737/10000] (13.90GB) Downloading: nationwidechildrens.org_ssf.TCGA-AC-A3TN.xml (0.01 MB)... "
80273
+ ]
80274
+ },
80275
+ {
80276
+ "name": "stdout",
80277
+ "output_type": "stream",
80278
+ "text": [
80279
+ "OK\n",
80280
+ "[9738/10000] (13.90GB) Downloading: TCGA-BRCA.0016bb20-f9ab-42ad-9d22-154bc12dfc14.ascat3.allelic_specific.seg.txt (0.00 MB)... "
80281
+ ]
80282
+ },
80283
+ {
80284
+ "name": "stdout",
80285
+ "output_type": "stream",
80286
+ "text": [
80287
+ "OK\n",
80288
+ "[9739/10000] (13.90GB) Downloading: NULLS_p_TCGA_183_185_186_SNP_N_GenomeWideSNP_6_E04_914174.nocnv_grch38.seg.v2.txt (0.01 MB)... "
80289
+ ]
80290
+ },
80291
+ {
80292
+ "name": "stdout",
80293
+ "output_type": "stream",
80294
+ "text": [
80295
+ "OK\n",
80296
+ "[9740/10000] (13.90GB) Downloading: TCGA-BRCA.7d50bbff-dd79-407c-8701-a42c332c404f.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
80297
+ ]
80298
+ },
80299
+ {
80300
+ "name": "stdout",
80301
+ "output_type": "stream",
80302
+ "text": [
80303
+ "OK\n",
80304
+ "[9741/10000] (13.90GB) Downloading: TCGA-BRCA.2def89d4-9863-4170-880b-4fec28a1465b.ascat2.allelic_specific.seg.txt (0.01 MB)... "
80305
+ ]
80306
+ },
80307
+ {
80308
+ "name": "stdout",
80309
+ "output_type": "stream",
80310
+ "text": [
80311
+ "OK\n",
80312
+ "[9742/10000] (13.90GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_D06_735366.nocnv_grch38.seg.v2.txt (0.01 MB)... "
80313
+ ]
80314
+ },
80315
+ {
80316
+ "name": "stdout",
80317
+ "output_type": "stream",
80318
+ "text": [
80319
+ "OK\n",
80320
+ "[9743/10000] (13.90GB) Downloading: nationwidechildrens.org_clinical.TCGA-AC-A3TN.xml (0.06 MB)... "
80321
+ ]
80322
+ },
80323
+ {
80324
+ "name": "stdout",
80325
+ "output_type": "stream",
80326
+ "text": [
80327
+ "OK\n",
80328
+ "[9744/10000] (13.90GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_B08_760346.nocnv_grch38.seg.v2.txt (0.00 MB)... "
80329
+ ]
80330
+ },
80331
+ {
80332
+ "name": "stdout",
80333
+ "output_type": "stream",
80334
+ "text": [
80335
+ "OK\n",
80336
+ "[9745/10000] (13.90GB) Downloading: 0b2aa006-2958-431c-917a-0d9b0c381f66_noid_Grn.idat (7.72 MB)... "
80337
+ ]
80338
+ },
80339
+ {
80340
+ "name": "stdout",
80341
+ "output_type": "stream",
80342
+ "text": [
80343
+ "OK\n",
80344
+ "[9746/10000] (13.91GB) Downloading: TCGA-BRCA.2def89d4-9863-4170-880b-4fec28a1465b.gene_level_copy_number.v36.tsv (3.29 MB)... "
80345
+ ]
80346
+ },
80347
+ {
80348
+ "name": "stdout",
80349
+ "output_type": "stream",
80350
+ "text": [
80351
+ "OK\n",
80352
+ "[9747/10000] (13.91GB) Downloading: TCGA-BRCA.7d50bbff-dd79-407c-8701-a42c332c404f.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
80353
+ ]
80354
+ },
80355
+ {
80356
+ "name": "stdout",
80357
+ "output_type": "stream",
80358
+ "text": [
80359
+ "OK\n",
80360
+ "[9748/10000] (13.91GB) Downloading: TCGA-BRCA.2def89d4-9863-4170-880b-4fec28a1465b.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
80361
+ ]
80362
+ },
80363
+ {
80364
+ "name": "stdout",
80365
+ "output_type": "stream",
80366
+ "text": [
80367
+ "OK\n",
80368
+ "[9749/10000] (13.92GB) Downloading: 20ad4de5-be7e-4d45-83f5-e34c47e48009_noid_Red.idat (0.69 MB)... "
80369
+ ]
80370
+ },
80371
+ {
80372
+ "name": "stdout",
80373
+ "output_type": "stream",
80374
+ "text": [
80375
+ "OK\n",
80376
+ "[9750/10000] (13.92GB) Downloading: TCGA-BRCA.0016bb20-f9ab-42ad-9d22-154bc12dfc14.ascat2.allelic_specific.seg.txt (0.01 MB)... "
80377
+ ]
80378
+ },
80379
+ {
80380
+ "name": "stdout",
80381
+ "output_type": "stream",
80382
+ "text": [
80383
+ "OK\n",
80384
+ "[9751/10000] (13.92GB) Downloading: TCGA-E2-A14O-01A-21-A13E-20_RPPA_data.tsv (0.02 MB)... "
80385
+ ]
80386
+ },
80387
+ {
80388
+ "name": "stdout",
80389
+ "output_type": "stream",
80390
+ "text": [
80391
+ "OK\n",
80392
+ "[9752/10000] (13.92GB) Downloading: KEBAB_p_TCGASNP_226_227_N_GenomeWideSNP_6_E02_1151484.grch38.seg.v2.txt (0.03 MB)... "
80393
+ ]
80394
+ },
80395
+ {
80396
+ "name": "stdout",
80397
+ "output_type": "stream",
80398
+ "text": [
80399
+ "OK\n",
80400
+ "[9753/10000] (13.92GB) Downloading: nationwidechildrens.org_clinical.TCGA-E2-A14O.xml (0.06 MB)... "
80401
+ ]
80402
+ },
80403
+ {
80404
+ "name": "stdout",
80405
+ "output_type": "stream",
80406
+ "text": [
80407
+ "OK\n",
80408
+ "[9754/10000] (13.92GB) Downloading: TCGA-BRCA.0016bb20-f9ab-42ad-9d22-154bc12dfc14.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
80409
+ ]
80410
+ },
80411
+ {
80412
+ "name": "stdout",
80413
+ "output_type": "stream",
80414
+ "text": [
80415
+ "OK\n",
80416
+ "[9755/10000] (13.92GB) Downloading: TCGA-BRCA.0016bb20-f9ab-42ad-9d22-154bc12dfc14.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
80417
+ ]
80418
+ },
80419
+ {
80420
+ "name": "stdout",
80421
+ "output_type": "stream",
80422
+ "text": [
80423
+ "OK\n",
80424
+ "[9756/10000] (13.92GB) Downloading: TCGA-E2-A14O-01A-31D-A895-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.17 MB)... "
80425
+ ]
80426
+ },
80427
+ {
80428
+ "name": "stdout",
80429
+ "output_type": "stream",
80430
+ "text": [
80431
+ "OK\n",
80432
+ "[9757/10000] (13.92GB) Downloading: DEVEL_p_TCGAb3_73_74_75_76_NSP_GenomeWideSNP_6_C05_1438336.grch38.seg.v2.txt (0.03 MB)... "
80433
+ ]
80434
+ },
80435
+ {
80436
+ "name": "stdout",
80437
+ "output_type": "stream",
80438
+ "text": [
80439
+ "OK\n",
80440
+ "[9758/10000] (13.92GB) Downloading: nationwidechildrens.org_ssf.TCGA-E2-A14O.xml (0.01 MB)... "
80441
+ ]
80442
+ },
80443
+ {
80444
+ "name": "stdout",
80445
+ "output_type": "stream",
80446
+ "text": [
80447
+ "OK\n",
80448
+ "[9759/10000] (13.92GB) Downloading: TCGA-BRCA.2e3fb75f-065e-4db0-bddf-8bcc6c7ace38.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
80449
+ ]
80450
+ },
80451
+ {
80452
+ "name": "stdout",
80453
+ "output_type": "stream",
80454
+ "text": [
80455
+ "OK\n",
80456
+ "[9760/10000] (13.93GB) Downloading: TCGA-E9-A249-01A-01-TSA.b0659a1b-2892-4680-9045-23445b67763f.svs (119.86 MB)... "
80457
+ ]
80458
+ },
80459
+ {
80460
+ "name": "stdout",
80461
+ "output_type": "stream",
80462
+ "text": [
80463
+ "OK\n",
80464
+ "[9761/10000] (14.04GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_E05_778034.grch38.seg.v2.txt (0.03 MB)... "
80465
+ ]
80466
+ },
80467
+ {
80468
+ "name": "stdout",
80469
+ "output_type": "stream",
80470
+ "text": [
80471
+ "OK\n",
80472
+ "[9762/10000] (14.04GB) Downloading: DEVEL_p_TCGAb3_73_74_75_76_NSP_GenomeWideSNP_6_C05_1438336.nocnv_grch38.seg.v2.txt (0.01 MB)... "
80473
+ ]
80474
+ },
80475
+ {
80476
+ "name": "stdout",
80477
+ "output_type": "stream",
80478
+ "text": [
80479
+ "OK\n",
80480
+ "[9763/10000] (14.04GB) Downloading: f77c8703-fae0-40e5-99b6-771f66ac6c33_noid_Grn.idat (7.72 MB)... "
80481
+ ]
80482
+ },
80483
+ {
80484
+ "name": "stdout",
80485
+ "output_type": "stream",
80486
+ "text": [
80487
+ "OK\n",
80488
+ "[9764/10000] (14.05GB) Downloading: TCGA-BRCA.31fad9a6-80ba-4ed8-862a-d8e17816c645.ascat3.allelic_specific.seg.txt (0.00 MB)... "
80489
+ ]
80490
+ },
80491
+ {
80492
+ "name": "stdout",
80493
+ "output_type": "stream",
80494
+ "text": [
80495
+ "OK\n",
80496
+ "[9765/10000] (14.05GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-EW-A1P0.xml (0.06 MB)... "
80497
+ ]
80498
+ },
80499
+ {
80500
+ "name": "stdout",
80501
+ "output_type": "stream",
80502
+ "text": [
80503
+ "OK\n",
80504
+ "[9766/10000] (14.05GB) Downloading: 54012443-c0c0-4358-a7b4-81a7a904eeaa_noid_Grn.idat (7.72 MB)... "
80505
+ ]
80506
+ },
80507
+ {
80508
+ "name": "stdout",
80509
+ "output_type": "stream",
80510
+ "text": [
80511
+ "OK\n",
80512
+ "[9767/10000] (14.06GB) Downloading: c44ddc23-7a57-4ed0-b864-c1b0d450224a.mirbase21.isoforms.quantification.txt (0.35 MB)... "
80513
+ ]
80514
+ },
80515
+ {
80516
+ "name": "stdout",
80517
+ "output_type": "stream",
80518
+ "text": [
80519
+ "OK\n",
80520
+ "[9768/10000] (14.06GB) Downloading: 070a3de5-9f8e-44e5-ba8c-92077fdeef26.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
80521
+ ]
80522
+ },
80523
+ {
80524
+ "name": "stdout",
80525
+ "output_type": "stream",
80526
+ "text": [
80527
+ "OK\n",
80528
+ "[9769/10000] (14.06GB) Downloading: TCGA-XX-A899-11A-04-TS4.3DFEA459-7489-418F-B7C0-CA480F6AF471.svs (71.09 MB)... "
80529
+ ]
80530
+ },
80531
+ {
80532
+ "name": "stdout",
80533
+ "output_type": "stream",
80534
+ "text": [
80535
+ "OK\n",
80536
+ "[9770/10000] (14.13GB) Downloading: e1f1e3de-a466-4cdf-89d2-3f5c0e86a304.mirbase21.isoforms.quantification.txt (0.32 MB)... "
80537
+ ]
80538
+ },
80539
+ {
80540
+ "name": "stdout",
80541
+ "output_type": "stream",
80542
+ "text": [
80543
+ "OK\n",
80544
+ "[9771/10000] (14.13GB) Downloading: TCGA-XX-A899-11A-01-TS1.31A99BA4-5148-428B-9D5E-2999334193C6.svs (59.32 MB)... "
80545
+ ]
80546
+ },
80547
+ {
80548
+ "name": "stdout",
80549
+ "output_type": "stream",
80550
+ "text": [
80551
+ "OK\n",
80552
+ "[9772/10000] (14.19GB) Downloading: TCGA-BRCA.31fad9a6-80ba-4ed8-862a-d8e17816c645.gene_level_copy_number.v36.tsv (3.29 MB)... "
80553
+ ]
80554
+ },
80555
+ {
80556
+ "name": "stdout",
80557
+ "output_type": "stream",
80558
+ "text": [
80559
+ "OK\n",
80560
+ "[9773/10000] (14.19GB) Downloading: TCGA-E9-A249-01Z-00-DX1.CA244384-FD89-44F6-8F94-A060A4C241CA.svs (1164.34 MB)... "
80561
+ ]
80562
+ },
80563
+ {
80564
+ "name": "stderr",
80565
+ "output_type": "stream",
80566
+ "text": [
80567
+ "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n"
80568
+ ]
80569
+ },
80570
+ {
80571
+ "name": "stdout",
80572
+ "output_type": "stream",
80573
+ "text": [
80574
+ "OK\n",
80575
+ "\n",
80576
+ "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
80577
+ "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.33 GB).\n",
80578
+ "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n",
80579
+ "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
80580
+ "\n"
80581
+ ]
80582
+ },
80583
+ {
80584
+ "data": {
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80588
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80589
+ },
80590
+ "text/plain": [
80591
+ "Processing Files (0 / 0): | | 0.00B / 0.00B "
80592
+ ]
80593
+ },
80594
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80595
+ "output_type": "display_data"
80596
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80597
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+ "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n",
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+ "[9774/10000] (15.33GB) Downloading: HEIGH_p_TCGAb418_19_21_BCR_NSP_GenomeWideSNP_6_G04_1485732.nocnv_grch38.seg.v2.txt (0.00 MB)... "
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+ "OK\n",
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+ "\n",
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+ "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
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+ "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.33 GB).\n",
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+ "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n",
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+ "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
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+ "\n"
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data/gdc_data_organized/3ecb0147-276d-486c-9af0-ce437c24ba83/10372e34-aeb4-4e7a-a7ca-71fb7c585d5d.mirbase21.isoforms.quantification.txt ADDED
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data/gdc_data_organized/3ecb0147-276d-486c-9af0-ce437c24ba83/8cf6a0f3-9dfb-41f5-b855-c313c583e707.rna_seq.augmented_star_gene_counts.tsv ADDED
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data/gdc_data_organized/3ecb0147-276d-486c-9af0-ce437c24ba83/TCGA-BRCA.b8ff6277-3c53-4912-ae50-8e82a94f7244.ascat3.allelic_specific.seg.txt ADDED
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1
+ <?xml version="1.0" encoding="UTF-8"?>
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16
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19
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45
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+ <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-11-A13C-20</bio:shipment_portion_bcr_aliquot_barcode>
59
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+ </bio:shipment_portion>
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63
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+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30.00</bio:weight>
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71
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+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
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74
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75
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76
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
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78
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81
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82
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83
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84
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85
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
86
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87
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88
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89
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90
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91
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92
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93
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94
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21D-A10X-02</bio:bcr_aliquot_barcode>
95
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96
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+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.08</bio:quantity>
98
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99
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
100
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+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
104
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106
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107
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108
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109
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110
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
111
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
112
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21D-A10Y-09</bio:bcr_aliquot_barcode>
113
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0a31d504-c1dc-4c85-8079-bf1756f2c281</bio:bcr_aliquot_uuid>
114
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.08</bio:concentration>
115
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.08</bio:quantity>
116
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</bio:volume>
117
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
118
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
119
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100490488</bio:biospecimen_barcode_bottom>
120
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
121
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
122
+ </bio:aliquot>
123
+ <bio:aliquot>
124
+ <admin:additional_studies/>
125
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A111</bio:plate_id>
126
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
127
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
128
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
129
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
130
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21D-A111-01</bio:bcr_aliquot_barcode>
131
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">b8ff6277-3c53-4912-ae50-8e82a94f7244</bio:bcr_aliquot_uuid>
132
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
133
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.07</bio:quantity>
134
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
135
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
136
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
137
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100487608</bio:biospecimen_barcode_bottom>
138
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
139
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
140
+ </bio:aliquot>
141
+ <bio:aliquot>
142
+ <admin:additional_studies/>
143
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A112</bio:plate_id>
144
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
145
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
146
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
147
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
148
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21D-A112-05</bio:bcr_aliquot_barcode>
149
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">dfdf4f91-7df2-4d84-92ce-86ce84c876a0</bio:bcr_aliquot_uuid>
150
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
151
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.27</bio:quantity>
152
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
153
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
154
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
155
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100488856</bio:biospecimen_barcode_bottom>
156
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
157
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
158
+ </bio:aliquot>
159
+ </bio:aliquots>
160
+ <bio:protocols>
161
+ <bio:protocol>
162
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
163
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
164
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
165
+ </bio:protocol>
166
+ </bio:protocols>
167
+ <bio:dna>
168
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
169
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
170
+ </bio:dna>
171
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
172
+ </bio:analyte>
173
+ <bio:analyte>
174
+ <admin:additional_studies/>
175
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
176
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
177
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
178
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
179
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.88</bio:a260_a280_ratio>
180
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
181
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
182
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21R</bio:bcr_analyte_barcode>
183
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c30e41f2-3a4f-4961-a0f8-8095ba8bbaaa</bio:bcr_analyte_uuid>
184
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
185
+ <bio:aliquots>
186
+ <bio:aliquot>
187
+ <admin:additional_studies/>
188
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A114</bio:plate_id>
189
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
190
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
191
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
192
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
193
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21R-A114-13</bio:bcr_aliquot_barcode>
194
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2197544f-4509-46ae-967d-ded0cf6a00e2</bio:bcr_aliquot_uuid>
195
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
196
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.00</bio:quantity>
197
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
198
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">F</bio:plate_row>
199
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
200
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099014272</bio:biospecimen_barcode_bottom>
201
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
202
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
203
+ </bio:aliquot>
204
+ <bio:aliquot>
205
+ <admin:additional_studies/>
206
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A115</bio:plate_id>
207
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">07</bio:center_id>
208
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
209
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
210
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
211
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21R-A115-07</bio:bcr_aliquot_barcode>
212
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0ef20000-2c8e-47bb-86e5-ffa2814099a7</bio:bcr_aliquot_uuid>
213
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
214
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.01</bio:quantity>
215
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
216
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">F</bio:plate_row>
217
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
218
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099020608</bio:biospecimen_barcode_bottom>
219
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
220
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
221
+ </bio:aliquot>
222
+ </bio:aliquots>
223
+ <bio:protocols>
224
+ <bio:protocol>
225
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
226
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
227
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
228
+ </bio:protocol>
229
+ </bio:protocols>
230
+ <bio:rna>
231
+ <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.60</bio:ratio_28s_18s>
232
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9.10</bio:rinvalue>
233
+ </bio:rna>
234
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
235
+ </bio:analyte>
236
+ <bio:analyte>
237
+ <admin:additional_studies/>
238
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
239
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
240
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
241
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
242
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
243
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
244
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
245
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21W</bio:bcr_analyte_barcode>
246
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C78BB504-92A3-420D-938F-FFA343C1B6C1</bio:bcr_analyte_uuid>
247
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
248
+ <bio:aliquots>
249
+ <bio:aliquot>
250
+ <admin:additional_studies/>
251
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A12T</bio:plate_id>
252
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
253
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
254
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
255
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
256
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-21W-A12T-09</bio:bcr_aliquot_barcode>
257
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">df82226e-2242-418b-9f5f-0a5e531826a4</bio:bcr_aliquot_uuid>
258
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
259
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
260
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
261
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
262
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
263
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108432433</bio:biospecimen_barcode_bottom>
264
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
265
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
266
+ </bio:aliquot>
267
+ </bio:aliquots>
268
+ <bio:protocols>
269
+ <bio:protocol>
270
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
271
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
272
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
273
+ </bio:protocol>
274
+ </bio:protocols>
275
+ <bio:dna>
276
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
277
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
278
+ </bio:dna>
279
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
280
+ </bio:analyte>
281
+ </bio:analytes>
282
+ <bio:slides>
283
+ <bio:slide>
284
+ <admin:additional_studies/>
285
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
286
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
287
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_cells>
288
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">60</bio:percent_tumor_nuclei>
289
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
290
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
291
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">19</bio:percent_stromal_cells>
292
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
293
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">4</bio:percent_lymphocyte_infiltration>
294
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
295
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
296
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
297
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
298
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-02-BSB</shared:bcr_slide_barcode>
299
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">63ea0e68-49cf-4897-834b-d11519db02ec</shared:bcr_slide_uuid>
300
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-BH-A0BR-01A-02-BSB.63ea0e68-49cf-4897-834b-d11519db02ec.svs</shared:image_file_name>
301
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
302
+ </bio:slide>
303
+ <bio:slide>
304
+ <admin:additional_studies/>
305
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
306
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
307
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_cells>
308
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">60</bio:percent_tumor_nuclei>
309
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
310
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
311
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">19</bio:percent_stromal_cells>
312
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
313
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">4</bio:percent_lymphocyte_infiltration>
314
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
315
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
316
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
317
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
318
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319
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+ </ssf:tumor_location>
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+ </ssf:tumor_locations>
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+ </ssf:tumor_sample>
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+ <ssf:ncedna_dna_vol preferred_name="normal_control_DNA_volume" display_order="49" cde="3288188" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1117174">80</ssf:ncedna_dna_vol>
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+ </ssf:normal_control_location>
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+ </ssf:normal_control_locations>
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+ </ssf:tcga_bcr>
data/gdc_data_organized/42621dfa-abfd-4c7d-8bc5-a02a09d1c2b4/062ca805-bac4-4f3d-98dc-92c03f8996c0.methylation_array.sesame.level3betas.txt ADDED
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data/gdc_data_organized/42621dfa-abfd-4c7d-8bc5-a02a09d1c2b4/GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_G10_735244.nocnv_grch38.seg.v2.txt ADDED
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data/gdc_data_organized/42621dfa-abfd-4c7d-8bc5-a02a09d1c2b4/TCGA-BRCA.6d730c4d-2c62-4214-aa35-f40126e65560.absolute_liftover.gene_level_copy_number.v36.tsv ADDED
The diff for this file is too large to render. See raw diff
 
data/gdc_data_organized/42621dfa-abfd-4c7d-8bc5-a02a09d1c2b4/TCGA-BRCA.6d730c4d-2c62-4214-aa35-f40126e65560.ascat3.allelic_specific.seg.txt ADDED
@@ -0,0 +1,140 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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2
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+ <admin:batch_number xsd_ver="1.17">85.87.0</admin:batch_number>
7
+ <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
8
+ <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
9
+ <admin:day_of_dcc_upload xsd_ver="1.17">6</admin:day_of_dcc_upload>
10
+ <admin:month_of_dcc_upload xsd_ver="1.17">11</admin:month_of_dcc_upload>
11
+ <admin:year_of_dcc_upload xsd_ver="1.17">2018</admin:year_of_dcc_upload>
12
+ <admin:program xsd_ver="2.7">TCGA</admin:program>
13
+ <admin:dbgap_registration_code xsd_ver="2.7">000178</admin:dbgap_registration_code>
14
+ </admin:admin>
15
+ <bio:patient>
16
+ <admin:additional_studies/>
17
+ <shared:bcr_patient_barcode cde="2003301" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z</shared:bcr_patient_barcode>
18
+ <shared:bcr_patient_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">42621dfa-abfd-4c7d-8bc5-a02a09d1c2b4</shared:bcr_patient_uuid>
19
+ <shared:tissue_source_site cde="" xsd_ver="2.4" procurement_status="Completed" owner="">C8</shared:tissue_source_site>
20
+ <shared:patient_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A12Z</shared:patient_id>
21
+ <shared:gender cde="2200604" xsd_ver="1.8" procurement_status="Completed" owner="">FEMALE</shared:gender>
22
+ <bio:days_to_index precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">0</bio:days_to_index>
23
+ <bio:bcr_canonical_check>
24
+ <bio:bcr_patient_canonical_status cde="" xsd_ver="2.6" procurement_status="Completed" owner="">Canonical</bio:bcr_patient_canonical_status>
25
+ </bio:bcr_canonical_check>
26
+ <bio:samples>
27
+ <bio:sample>
28
+ <admin:additional_studies/>
29
+ <bio:specimen_fraction_ordinal cde="" xsd_ver="2.7" procurement_status="Not Available" owner=""/>
30
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:sample_type_id>
31
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
32
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
33
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Primary Tumor</bio:sample_type>
34
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
35
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
36
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
37
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">490</bio:initial_weight>
38
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
39
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
40
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">true</bio:oct_embedded>
41
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
42
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
43
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
44
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
45
+ <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">69</bio:days_to_collection>
46
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
47
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
48
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A</bio:bcr_sample_barcode>
49
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">238ffa7f-eecf-4f46-8831-efa0d23fa66c</bio:bcr_sample_uuid>
50
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
51
+ <bio:portions>
52
+ <bio:shipment_portion>
53
+ <admin:additional_studies/>
54
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">21</bio:portion_number>
55
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2</bio:portion_sequence>
56
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A13D</bio:plate_id>
57
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">20</bio:center_id>
58
+ <bio:shipment_portion_day_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">22</bio:shipment_portion_day_of_shipment>
59
+ <bio:shipment_portion_month_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">3</bio:shipment_portion_month_of_shipment>
60
+ <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2011</bio:shipment_portion_year_of_shipment>
61
+ <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-21-A13D-20</bio:shipment_portion_bcr_aliquot_barcode>
62
+ <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">76306f2d-c820-4442-966f-b79872d69025</bio:bcr_shipment_portion_uuid>
63
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
64
+ </bio:shipment_portion>
65
+ <bio:shipment_portion>
66
+ <admin:additional_studies/>
67
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">41</bio:portion_number>
68
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4</bio:portion_sequence>
69
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A21V</bio:plate_id>
70
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">30</bio:center_id>
71
+ <bio:shipment_portion_day_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">3</bio:shipment_portion_day_of_shipment>
72
+ <bio:shipment_portion_month_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">4</bio:shipment_portion_month_of_shipment>
73
+ <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2012</bio:shipment_portion_year_of_shipment>
74
+ <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-41-A21V-30</bio:shipment_portion_bcr_aliquot_barcode>
75
+ <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">26C6D77F-B2D2-4B3D-B3DE-E4BA833043FC</bio:bcr_shipment_portion_uuid>
76
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
77
+ </bio:shipment_portion>
78
+ <bio:portion>
79
+ <admin:additional_studies/>
80
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">11</bio:portion_number>
81
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
82
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:day_of_creation>
83
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:month_of_creation>
84
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
85
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30.00</bio:weight>
86
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11</bio:bcr_portion_barcode>
87
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">369d505b-fe26-4d88-b91f-c4adcb97f310</bio:bcr_portion_uuid>
88
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
89
+ <bio:analytes>
90
+ <bio:analyte>
91
+ <admin:additional_studies/>
92
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
93
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
94
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
95
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.12</bio:concentration>
96
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
97
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
98
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
99
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11D</bio:bcr_analyte_barcode>
100
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">77dfe9d3-a103-47d5-878f-0bed94911403</bio:bcr_analyte_uuid>
101
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
102
+ <bio:aliquots>
103
+ <bio:aliquot>
104
+ <admin:additional_studies/>
105
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A10X</bio:plate_id>
106
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
107
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
108
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
109
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
110
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11D-A10X-02</bio:bcr_aliquot_barcode>
111
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">295996bc-f2bd-4804-8b16-763572ed35a7</bio:bcr_aliquot_uuid>
112
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.12</bio:concentration>
113
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.56</bio:quantity>
114
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
115
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
116
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
117
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100490614</bio:biospecimen_barcode_bottom>
118
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
119
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
120
+ </bio:aliquot>
121
+ <bio:aliquot>
122
+ <admin:additional_studies/>
123
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A10Y</bio:plate_id>
124
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
125
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
126
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
127
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
128
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11D-A10Y-09</bio:bcr_aliquot_barcode>
129
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ae68cac5-e561-4094-98fa-2303cdaa6dbb</bio:bcr_aliquot_uuid>
130
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.06</bio:concentration>
131
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.56</bio:quantity>
132
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</bio:volume>
133
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
134
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
135
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100490518</bio:biospecimen_barcode_bottom>
136
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
137
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
138
+ </bio:aliquot>
139
+ <bio:aliquot>
140
+ <admin:additional_studies/>
141
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A111</bio:plate_id>
142
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
143
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
144
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
145
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
146
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11D-A111-01</bio:bcr_aliquot_barcode>
147
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6d730c4d-2c62-4214-aa35-f40126e65560</bio:bcr_aliquot_uuid>
148
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.12</bio:concentration>
149
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.80</bio:quantity>
150
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
151
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
152
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
153
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100487638</bio:biospecimen_barcode_bottom>
154
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
155
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
156
+ </bio:aliquot>
157
+ <bio:aliquot>
158
+ <admin:additional_studies/>
159
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A112</bio:plate_id>
160
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
161
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
162
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
163
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
164
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11D-A112-05</bio:bcr_aliquot_barcode>
165
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">d1074588-bd51-4d39-9cb2-e5e6a622f9b5</bio:bcr_aliquot_uuid>
166
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.12</bio:concentration>
167
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.20</bio:quantity>
168
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
169
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
170
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
171
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100488886</bio:biospecimen_barcode_bottom>
172
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
173
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
174
+ </bio:aliquot>
175
+ </bio:aliquots>
176
+ <bio:protocols>
177
+ <bio:protocol>
178
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
179
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
180
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
181
+ </bio:protocol>
182
+ </bio:protocols>
183
+ <bio:dna>
184
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
185
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
186
+ </bio:dna>
187
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">PicoGreen</bio:spectrophotometer_method>
188
+ </bio:analyte>
189
+ <bio:analyte>
190
+ <admin:additional_studies/>
191
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
192
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
193
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
194
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
195
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.82</bio:a260_a280_ratio>
196
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
197
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
198
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11R</bio:bcr_analyte_barcode>
199
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1035a351-ec13-44be-922d-9095317c52a2</bio:bcr_analyte_uuid>
200
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
201
+ <bio:aliquots>
202
+ <bio:aliquot>
203
+ <admin:additional_studies/>
204
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A114</bio:plate_id>
205
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
206
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
207
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
208
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
209
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11R-A114-13</bio:bcr_aliquot_barcode>
210
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">74d155b4-3527-4b8d-b050-21670f3b6027</bio:bcr_aliquot_uuid>
211
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
212
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.20</bio:quantity>
213
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
214
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
215
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
216
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099014263</bio:biospecimen_barcode_bottom>
217
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
218
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
219
+ </bio:aliquot>
220
+ <bio:aliquot>
221
+ <admin:additional_studies/>
222
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A115</bio:plate_id>
223
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">07</bio:center_id>
224
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
225
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
226
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
227
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11R-A115-07</bio:bcr_aliquot_barcode>
228
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4018d26c-0ce0-4c5a-9ce4-200bb4273349</bio:bcr_aliquot_uuid>
229
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
230
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.27</bio:quantity>
231
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
232
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
233
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
234
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099020599</bio:biospecimen_barcode_bottom>
235
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
236
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
237
+ </bio:aliquot>
238
+ </bio:aliquots>
239
+ <bio:protocols>
240
+ <bio:protocol>
241
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
242
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
243
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
244
+ </bio:protocol>
245
+ </bio:protocols>
246
+ <bio:rna>
247
+ <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.70</bio:ratio_28s_18s>
248
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9.60</bio:rinvalue>
249
+ </bio:rna>
250
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
251
+ </bio:analyte>
252
+ <bio:analyte>
253
+ <admin:additional_studies/>
254
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
255
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
256
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
257
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
258
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
259
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
260
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
261
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11W</bio:bcr_analyte_barcode>
262
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4FCCE843-363D-46E9-B02C-441BE3F15ACE</bio:bcr_analyte_uuid>
263
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
264
+ <bio:aliquots>
265
+ <bio:aliquot>
266
+ <admin:additional_studies/>
267
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A12T</bio:plate_id>
268
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
269
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
270
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
271
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
272
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-11W-A12T-09</bio:bcr_aliquot_barcode>
273
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ad83443d-4a7e-4d0d-96e4-7c2f8b5eda4b</bio:bcr_aliquot_uuid>
274
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
275
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
276
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
277
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
278
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
279
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108432463</bio:biospecimen_barcode_bottom>
280
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
281
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
282
+ </bio:aliquot>
283
+ </bio:aliquots>
284
+ <bio:protocols>
285
+ <bio:protocol>
286
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
287
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
288
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
289
+ </bio:protocol>
290
+ </bio:protocols>
291
+ <bio:dna>
292
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
293
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
294
+ </bio:dna>
295
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
296
+ </bio:analyte>
297
+ </bio:analytes>
298
+ <bio:slides>
299
+ <bio:slide>
300
+ <admin:additional_studies/>
301
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
302
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
303
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">60</bio:percent_tumor_cells>
304
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">60</bio:percent_tumor_nuclei>
305
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
306
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:percent_necrosis>
307
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:percent_stromal_cells>
308
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
309
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">40</bio:percent_lymphocyte_infiltration>
310
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_monocyte_infiltration>
311
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
312
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_neutrophil_infiltration>
313
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
314
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-01-BSA</shared:bcr_slide_barcode>
315
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">e7ddd80e-4b44-49f3-ac1c-4cf2b061c0a6</shared:bcr_slide_uuid>
316
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-01-BSA.e7ddd80e-4b44-49f3-ac1c-4cf2b061c0a6.svs</shared:image_file_name>
317
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
318
+ </bio:slide>
319
+ <bio:slide>
320
+ <admin:additional_studies/>
321
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
322
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
323
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">40</bio:percent_tumor_cells>
324
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">40</bio:percent_tumor_nuclei>
325
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
326
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_necrosis>
327
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">40</bio:percent_stromal_cells>
328
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
329
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">40</bio:percent_lymphocyte_infiltration>
330
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_monocyte_infiltration>
331
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
332
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_neutrophil_infiltration>
333
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
334
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-01-TSA</shared:bcr_slide_barcode>
335
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">d85a700f-8886-4b59-8ceb-d1d8e15fdd19</shared:bcr_slide_uuid>
336
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-C8-A12Z-01A-01-TSA.d85a700f-8886-4b59-8ceb-d1d8e15fdd19.svs</shared:image_file_name>
337
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
338
+ </bio:slide>
339
+ </bio:slides>
340
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
341
+ </bio:portion>
342
+ </bio:portions>
343
+ <bio:tumor_pathology/>
344
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
345
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
346
+ <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
347
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">89B312D1-9FDD-4756-9C15-5442B428F75A</bio:pathology_report_uuid>
348
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-C8-A12Z.89B312D1-9FDD-4756-9C15-5442B428F75A.pdf</bio:pathology_report_file_name>
349
+ <bio:diagnostic_slides>
350
+ <admin:additional_studies/>
351
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">22616420-7C80-42DE-9C44-0F00327681C6</bio:ffpe_slide_uuid>
352
+ </bio:diagnostic_slides>
353
+ </bio:sample>
354
+ <bio:sample>
355
+ <admin:additional_studies/>
356
+ <bio:specimen_fraction_ordinal cde="" xsd_ver="2.7" procurement_status="Not Available" owner=""/>
357
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
358
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
359
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
360
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
361
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
362
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
363
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
364
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
365
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
366
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
367
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
368
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
369
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
370
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
371
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
372
+ <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">69</bio:days_to_collection>
373
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
374
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
375
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-10A</bio:bcr_sample_barcode>
376
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">debff785-4321-463f-89f2-40a6214ffa14</bio:bcr_sample_uuid>
377
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
378
+ <bio:portions>
379
+ <bio:portion>
380
+ <admin:additional_studies/>
381
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
382
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
383
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:day_of_creation>
384
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:month_of_creation>
385
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
386
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2.00</bio:weight>
387
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-10A-01</bio:bcr_portion_barcode>
388
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2d46f347-8379-4de9-817b-6524713004c5</bio:bcr_portion_uuid>
389
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
390
+ <bio:analytes>
391
+ <bio:analyte>
392
+ <admin:additional_studies/>
393
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
394
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
395
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
396
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
397
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.98</bio:a260_a280_ratio>
398
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
399
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
400
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-10A-01D</bio:bcr_analyte_barcode>
401
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">b6eb3069-cfc9-4102-8115-a0ca8d99e867</bio:bcr_analyte_uuid>
402
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
403
+ <bio:aliquots>
404
+ <bio:aliquot>
405
+ <admin:additional_studies/>
406
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A10Z</bio:plate_id>
407
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
408
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
409
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
410
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
411
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A12Z-10A-01D-A10Z-02</bio:bcr_aliquot_barcode>
412
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">cf4bf84a-c678-426d-8a94-801ab47a45ad</bio:bcr_aliquot_uuid>
413
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
414
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.08</bio:quantity>
415
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
416
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
417
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
418
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100490806</bio:biospecimen_barcode_bottom>
419
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
420
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
421
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data/gdc_data_organized/6020d1b4-ee20-4cc9-82a3-340b5e3122f1/nationwidechildrens.org_ssf.TCGA-D8-A27L.xml ADDED
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+ <shared:maximum_tumor_dimension preferred_name="tumor_resected_max_dimension" display_order="9999" cde="64215" cde_ver="3.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
34
+ <ssf:tumor_weight preferred_name="tumor_sample_weight" display_order="23" cde="3081946" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895130">260</ssf:tumor_weight>
35
+ <ssf:sample_prescreened preferred_name="tumor_sample_prescreened_at_tss" display_order="19" cde="3081942" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895133">YES</ssf:sample_prescreened>
36
+ <shared:tumor_nuclei_percent preferred_name="tumor_nuclei_percent" display_order="24" cde="2841225" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895131">70</shared:tumor_nuclei_percent>
37
+ <shared:tumor_necrosis_percent preferred_name="necrosis_percent" display_order="25" cde="2841237" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895132">1</shared:tumor_necrosis_percent>
38
+ <ssf:days_to_pathology_review precision="day" xsd_ver="2.5" tier="2" cde="3288497" owner="TSS" procurement_status="Completed" preferred_name="tss_pathology_review_days_to" display_order="63" cde_ver="1.000">78</ssf:days_to_pathology_review>
39
+ <ssf:path_confirm_tumor_nuclei_metrics preferred_name="tumor_nuclei_requirements_indicator" display_order="64" cde="3288520" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895254">YES</ssf:path_confirm_tumor_nuclei_metrics>
40
+ <ssf:path_confirm_tumor_necrosis_metrics preferred_name="necrosis_requirements_indicator" display_order="65" cde="3288524" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895255">YES</ssf:path_confirm_tumor_necrosis_metrics>
41
+ <ssf:path_confirm_report_attached preferred_name="tss_pathology_submitted" display_order="66" cde="3288292" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895257">YES</ssf:path_confirm_report_attached>
42
+ <ssf:path_confirm_diagnosis_matching preferred_name="histologic_dx_consistent" display_order="68" cde="3288300" cde_ver="1.000" xsd_ver="1.8" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895256">YES</ssf:path_confirm_diagnosis_matching>
43
+ <ssf:reason_path_confirm_diagnosis_not_matching preferred_name="histologic_dx_inconsistent_reason" display_order="69" cde="3288315" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
44
+ <ssf:top_slide_submitted preferred_name="tumor_sample_top_slide_submitted" display_order="999" cde="3081944" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895134">YES</ssf:top_slide_submitted>
45
+ <ssf:digital_image_submitted preferred_name="tumor_sample_image_submitted" display_order="999" cde="3081948" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895135">NO</ssf:digital_image_submitted>
46
+ <ssf:ffpe_tumor_slide_submitted preferred_name="ffpe_slide_submitted_indicator" display_order="9999" cde="3295811" cde_ver="1.000" xsd_ver="2.5" tier="" owner="TSS" procurement_status="Completed" restricted="false">NO</ssf:ffpe_tumor_slide_submitted>
47
+ <ssf:submitted_for_lce preferred_name="tumor_sample_bcr_macrodissection" display_order="9999" cde="3288488" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
48
+ <shared:other_dx preferred_name="history_other_malignancy" display_order="14" cde="3382736" cde_ver="2.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895259">No</shared:other_dx>
49
+ <shared:history_of_neoadjuvant_treatment preferred_name="history_neoadjuvant_treatment" display_order="15" cde="3382737" cde_ver="1.000" xsd_ver="2.4" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895260">No</shared:history_of_neoadjuvant_treatment>
50
+ <shared:consent_or_death_status preferred_name="patient_consent_status" display_order="72" cde="3288361" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895261">Consented</shared:consent_or_death_status>
51
+ <shared:days_to_consent precision="day" xsd_ver="2.5" tier="1" cde="3288498" owner="TSS" procurement_status="Completed" preferred_name="patient_consent_days_to" display_order="76" cde_ver="1.000">33</shared:days_to_consent>
52
+ <shared:country preferred_name="tumor_sample_procurement_country" display_order="13" cde="3203072" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895127">Poland</shared:country>
53
+ <ssf_disease:disease_details/>
54
+ <ssf:tumor_histologies>
55
+ <ssf:tumor_histology>
56
+ <shared:histological_type preferred_name="histologic_diagnosis" display_order="3" cde="3081934" cde_ver="3.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895118">Infiltrating Ductal Carcinoma</shared:histological_type>
57
+ <shared:histological_type_other preferred_name="histologic_diagnosis_other" display_order="31" cde="3124492" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
58
+ <shared:histological_percentage preferred_name="histologic_diagnosis_percent" display_order="9999" cde="3729998" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
59
+ <shared:tumor_morphology_percentage preferred_name="" display_order="9999" cde="3729984" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
60
+ </ssf:tumor_histology>
61
+ </ssf:tumor_histologies>
62
+ <ssf:tumor_locations>
63
+ <ssf:tumor_focality preferred_name="tumor_focality" display_order="9999" cde="3174022" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
64
+ <ssf:laterality preferred_name="" display_order="9999" cde="4742852" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895121">Right</ssf:laterality>
65
+ <ssf:tumor_location>
66
+ <ssf:site_of_disease preferred_name="" display_order="9999" cde="4742851" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895121">Breast</ssf:site_of_disease>
67
+ <ssf:site_of_disease_text preferred_name="" display_order="9999" cde="4742871" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
68
+ <ssf:site_of_disease_description preferred_name="" display_order="9999" cde="4742918" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="895121"/>
69
+ </ssf:tumor_location>
70
+ </ssf:tumor_locations>
71
+ </ssf:tumor_sample>
72
+ </ssf:tumor_samples>
73
+ <ssf:normal_controls>
74
+ <ssf:normal_control>
75
+ <ssf:bcr_sample_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false">baa27db8-cce7-4c5a-8585-9ecb0041c4f7</ssf:bcr_sample_uuid>
76
+ <ssf:method_of_normal_sample_procurement preferred_name="normal_control_method" display_order="50" cde="3288147" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="895188">Blood Draw</ssf:method_of_normal_sample_procurement>
77
+ <ssf:other_method_of_normal_sample_procurement preferred_name="normal_control_method_other" display_order="51" cde="3288151" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="895189"/>
78
+ <ssf:days_to_normal_sample_procurement precision="day" xsd_ver="2.3" tier="1" cde="3288496" owner="TSS" procurement_status="Completed" preferred_name="normal_control_procurement_days_to" display_order="55" cde_ver="1.000">33</ssf:days_to_normal_sample_procurement>
79
+ <ssf:normal_sample_site_proximity_to_tumor preferred_name="normal_control_proximity_to_tumor" display_order="59" cde="3088708" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="895190"/>
80
+ <ssf:ncedna_dna_conc preferred_name="normal_control_DNA_concentration" display_order="48" cde="3288187" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="895181"/>
81
+ <ssf:ncedna_dna_qm preferred_name="normal_control_DNA_quant_method" display_order="47" cde="3288186" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="895180"/>
82
+ <ssf:ncedna_dna_qty preferred_name="normal_control_DNA_quantity" display_order="46" cde="3288185" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="895179"/>
83
+ <ssf:ncedna_dna_vol preferred_name="normal_control_DNA_volume" display_order="49" cde="3288188" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="895182"/>
84
+ <ssf:normal_control_locations>
85
+ <ssf:normal_control_location>
86
+ <ssf:normal_tissue_anatomic_site preferred_name="" display_order="57" cde="4132152" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="895183"/>
87
+ <ssf:other_anatomic_site_normal_tissue preferred_name="normal_control_site_other" display_order="58" cde="3288189" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="895184"/>
88
+ </ssf:normal_control_location>
89
+ </ssf:normal_control_locations>
90
+ </ssf:normal_control>
91
+ </ssf:normal_controls>
92
+ </ssf:patient>
93
+ </ssf:tcga_bcr>