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!Sample_geo_accession "GSM2528085" "GSM2528086" "GSM2528220" "GSM2528263" "GSM2528297" "GSM2528305" "GSM2528307" "GSM2528320" "GSM2528324" "GSM2528325" "GSM2528341" "GSM2528345" "GSM2528347" "GSM2528349" "GSM2528365" "GSM2528392" "GSM2528404" "GSM2528410" "GSM2528419" "GSM2528433" "GSM2528437" "GSM2528439" "GSM2528441"... |
!Sample_status "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12 2018" "Public on Mar 12... |
!Sample_submission_date "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "Mar 09 2017" "M... |
!Sample_last_update_date "May 04 2022" "Mar 12 2018" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "May 04 2022" "... |
!Sample_type "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "SRA" "... |
!Sample_channel_count "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1... |
!Sample_source_name_ch1 "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumor" "Primary breast tumo... |
!Sample_organism_ch1 "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"... |
!Sample_characteristics_ch1 "scan-b external id: Q008861.C008874.S000184.l2.r.m.c.lib.g.k.a.t" "scan-b external id: Q008860.C008864.S000189.l2.r.m2.c.lib.g.k.a.t" "scan-b external id: Q007079.C007100.S002089.l.r.m.c.lib.g.k.a.t" "scan-b external id: Q007294.C007301.S001422.l.r.m.c.lib.g.k.a.t" "scan-b external id: Q006... |
!Sample_characteristics_ch1 "instrument model: NextSeq 500" "instrument model: NextSeq 500" "instrument model: NextSeq 500" "instrument model: NextSeq 500" "instrument model: NextSeq 500" "instrument model: NextSeq 500" "instrument model: NextSeq 500" "instrument model: NextSeq 500" "instrument model: NextSeq 500" "ins... |
!Sample_characteristics_ch1 "age at diagnosis: 58" "age at diagnosis: 56" "age at diagnosis: 46" "age at diagnosis: 45" "age at diagnosis: 81" "age at diagnosis: 42" "age at diagnosis: 61" "age at diagnosis: 50" "age at diagnosis: 52" "age at diagnosis: 26" "age at diagnosis: 64" "age at diagnosis: 70" "age at diagnosi... |
!Sample_characteristics_ch1 "tumor size: 18" "tumor size: 24" "tumor size: 2" "tumor size: 13" "tumor size: 17" "tumor size: 11" "tumor size: 22" "tumor size: 30" "tumor size: 11" "tumor size: 7" "tumor size: 15" "tumor size: 17" "tumor size: 33" "tumor size: 7" "tumor size: 45" "tumor size: 17" "tumor size: 16" "tumor... |
!Sample_characteristics_ch1 "lymph node group: NodeNegative" "lymph node group: 1to3" "lymph node group: NodeNegative" "lymph node group: NodeNegative" "lymph node group: NodeNegative" "lymph node group: 1to3" "lymph node group: 1to3" "lymph node group: 1to3" "lymph node group: 1to3" "lymph node group: 1to3" "lymph nod... |
!Sample_characteristics_ch1 "lymph node status: NodeNegative" "lymph node status: NodePositive" "lymph node status: NodeNegative" "lymph node status: NodeNegative" "lymph node status: NodeNegative" "lymph node status: NodePositive" "lymph node status: NodePositive" "lymph node status: NodePositive" "lymph node status: ... |
!Sample_characteristics_ch1 "er status: 1" "er status: 1" "er status: NA" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 0" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 1" "er status: 0" "er st... |
!Sample_characteristics_ch1 "pgr status: NA" "pgr status: 1" "pgr status: NA" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: NA" "pgr status: 0" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: 1" "pgr status: 1" "... |
!Sample_characteristics_ch1 "her2 status: 0" "her2 status: 0" "her2 status: NA" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 1" "her2 status: 1" "her2 status: 0" "her2 status: 1" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 0" "her2 status: 0" "h... |
!Sample_characteristics_ch1 "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: 1" "ki67 status: NA" "ki67 status: 1" "ki67 status: NA" "ki67 status: NA" "ki67 status: NA" "ki67 status: 0" "ki67 s... |
!Sample_characteristics_ch1 "nhg: G2" "nhg: G2" "nhg: G3" "nhg: G2" "nhg: G2" "nhg: G3" "nhg: G3" "nhg: NA" "nhg: G2" "nhg: NA" "nhg: G2" "nhg: G3" "nhg: G1" "nhg: G1" "nhg: G1" "nhg: G2" "nhg: G3" "nhg: G2" "nhg: G3" "nhg: G2" "nhg: G2" "nhg: G2" "nhg: G2" "nhg: G2" "nhg: G3" "nhg: G3" "nhg: G2" "nhg: G1" "nhg: G3" "n... |
!Sample_characteristics_ch1 "er prediction mgc: 0" "er prediction mgc: 1" "er prediction mgc: 0" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 1" "er prediction mgc: 0" "er prediction m... |
!Sample_characteristics_ch1 "pgr prediction mgc: 0" "pgr prediction mgc: 1" "pgr prediction mgc: 0" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 1" "pgr prediction mgc: 0" "pgr... |
!Sample_characteristics_ch1 "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction mgc: 0" "her2 prediction ... |
!Sample_characteristics_ch1 "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 1" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction mgc: 0" "ki67 prediction ... |
!Sample_characteristics_ch1 "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G3" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction mgc: G2" "nhg prediction m... |
!Sample_characteristics_ch1 "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 0" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction sgc: 1" "er prediction s... |
!Sample_characteristics_ch1 "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 0" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr prediction sgc: 1" "pgr... |
!Sample_characteristics_ch1 "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 1" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction sgc: 0" "her2 prediction ... |
!Sample_characteristics_ch1 "ki67 prediction sgc: 0" "ki67 prediction sgc: 0" "ki67 prediction sgc: 1" "ki67 prediction sgc: 1" "ki67 prediction sgc: 0" "ki67 prediction sgc: 1" "ki67 prediction sgc: 1" "ki67 prediction sgc: 1" "ki67 prediction sgc: 0" "ki67 prediction sgc: 1" "ki67 prediction sgc: 0" "ki67 prediction ... |
!Sample_characteristics_ch1 "pam50 subtype: Normal" "pam50 subtype: Normal" "pam50 subtype: Basal" "pam50 subtype: LumA" "pam50 subtype: LumA" "pam50 subtype: LumA" "pam50 subtype: LumB" "pam50 subtype: Her2" "pam50 subtype: LumA" "pam50 subtype: LumB" "pam50 subtype: LumA" "pam50 subtype: Her2" "pam50 subtype: LumA" "... |
!Sample_characteristics_ch1 "overall survival days: 2410" "overall survival days: 2388" "overall survival days: 1893" "overall survival days: 1950" "overall survival days: 1881" "overall survival days: 1852" "overall survival days: 1885" "overall survival days: 1632" "overall survival days: 1593" "overall survival days... |
!Sample_characteristics_ch1 "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall survival event: 0" "overall sur... |
!Sample_characteristics_ch1 "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 0" "endocrine treated: 1" "endocrine treated: 0" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 1" "endocrine treated: 0" "endocrine treat... |
!Sample_characteristics_ch1 "chemo treated: 0" "chemo treated: 1" "chemo treated: 0" "chemo treated: 0" "chemo treated: 0" "chemo treated: 1" "chemo treated: 1" "chemo treated: 1" "chemo treated: 1" "chemo treated: 1" "chemo treated: 0" "chemo treated: 1" "chemo treated: 1" "chemo treated: 0" "chemo treated: 0" "chemo ... |
!Sample_molecule_ch1 "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA" "polyA RNA"... |
!Sample_extract_protocol_ch1 "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "QIAGEN AllPrep" "Q... |
!Sample_extract_protocol_ch1 "Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the frag... |
!Sample_taxid_ch1 "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "9606" "... |
!Sample_description "ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high" "ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high" "ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high" "ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high" "ER/PgR/HER2/Ki67: 0 neg... |
!Sample_description "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "processed data file:" "... |
!Sample_description "gene_expression_3273_samples_and_136_replicates_transformed.csv" "gene_expression_3273_samples_and_136_replicates_transformed.csv" "gene_expression_3273_samples_and_136_replicates_transformed.csv" "gene_expression_3273_samples_and_136_replicates_transformed.csv" "gene_expression_3273_samples_and_13... |
!Sample_description "transcript_expression_3273_samples_and_136_replicates.csv" "transcript_expression_3273_samples_and_136_replicates.csv" "transcript_expression_3273_samples_and_136_replicates.csv" "transcript_expression_3273_samples_and_136_replicates.csv" "transcript_expression_3273_samples_and_136_replicates.csv" ... |
!Sample_data_processing "Base-calling using manufacturer's on-instrument software." "Base-calling using manufacturer's on-instrument software." "Base-calling using manufacturer's on-instrument software." "Base-calling using manufacturer's on-instrument software." "Base-calling using manufacturer's on-instrument softwar... |
!Sample_data_processing "Demultiplexing was done with Picard versions 1.120 or 1.128. IlluminaBasecallsToFastq parameters used were ADAPTERS_TO_CHECK=INDEXED, ADAPTERS_TO_CHECK=PAIRED_END, INCLUDE_NON_PF_READS=false" "Demultiplexing was done with Picard versions 1.120 or 1.128. IlluminaBasecallsToFastq parameters used ... |
!Sample_data_processing "Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC Rep... |
!Sample_data_processing "Fragment size distribution (mean and width) for the alignment step was estimated for each sample using bowtie2 2.2.3 and 2.2.5. Parameter set during estimation were -fr, -k 1, --phred33, --local, and -u 100000, using human genome assembly GRCh38." "Fragment size distribution (mean and width) fo... |
!Sample_data_processing "Remaining reads were aligned using TopHat2 2.0.12 or 2.0.13 (default parameters except for --mate-inner-dist X (estimated in previous step), --mate-std-dev Y (estimated in previous step), --library-type fr-firststrand, --no-coverage-search, --max-insertion-length 20, --max-deletion-length 20, -... |
!Sample_data_processing "Gene expression data in FPKM were generated using cufflinks 2.2.1 (default parameters except –GTF, --frag-bias-correct GRCh38.fa, --multi-read-correct, --library-type fr-firststrand, --total-hits-norm, --max-bundle-frags 10000000). The resulting data was was post-processed by collapsing on 30,8... |
!Sample_data_processing "PAM50 subtyping was performed using an implementation of the Parker method (Parker et al., J.Clin Oncol 2009). In short, to avoid context dependency when assigning PAM50 subtype by nearest-centroid, a fixed reference was selected to match the original cohort used by Parker et al. with respect t... |
!Sample_data_processing "Single-gene classifiers (SGCs) and multi-gene classifiers (MGCs) were trained for ER, PgR, HER2, Ki67 (SGC and MGC) and NHG (MGC only) on the expression of the single underlying gene (ESR1, PGR, ERBB2 or MKI67) or multiple genes (5000 most varying genes across all samples) of a 405 sample cohor... |
!Sample_data_processing "Genome_build: Human genome reference GRCh38/hg38." "Genome_build: Human genome reference GRCh38/hg38." "Genome_build: Human genome reference GRCh38/hg38." "Genome_build: Human genome reference GRCh38/hg38." "Genome_build: Human genome reference GRCh38/hg38." "Genome_build: Human genome referenc... |
!Sample_data_processing "Supplementary_files_format_and_content: Gene expression in FPKM in CSV format." "Supplementary_files_format_and_content: Gene expression in FPKM in CSV format." "Supplementary_files_format_and_content: Gene expression in FPKM in CSV format." "Supplementary_files_format_and_content: Gene express... |
!Sample_platform_id "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GPL18573" "GP... |
!Sample_contact_name "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" "Lao,H,Saal" ... |
!Sample_contact_email "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao.saal@med.lu.se" "lao... |
!Sample_contact_laboratory "Translational Oncogenomics Unit" "Translational Oncogenomics Unit" "Translational Oncogenomics Unit" "Translational Oncogenomics Unit" "Translational Oncogenomics Unit" "Translational Oncogenomics Unit" "Translational Oncogenomics Unit" "Translational Oncogenomics Unit" "Translational Oncoge... |
!Sample_contact_department "Department of Oncology and Pathology" "Department of Oncology and Pathology" "Department of Oncology and Pathology" "Department of Oncology and Pathology" "Department of Oncology and Pathology" "Department of Oncology and Pathology" "Department of Oncology and Pathology" "Department of Oncol... |
!Sample_contact_institute "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund University" "Lund ... |
!Sample_contact_address "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevägen 2, MV404B2" "Scheelevä... |
!Sample_contact_city "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund" "Lund... |
!Sample_contact_zip/postal_code "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" "22391" ... |
!Sample_contact_country "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden" "Sweden"... |
!Sample_data_row_count "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "0" "... |
!Sample_instrument_model "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 500" "Illumina NextSeq 5... |
!Sample_library_selection "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" "cDNA" ... |
!Sample_library_source "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcriptomic" "transcr... |
!Sample_library_strategy "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-... |
!Sample_relation "Reanalyzed by: GSM6103162" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06556980" "Reanalyzed by: GSM6104251" "Reanalyzed by: GSM6104069" "Reanalyzed by: GSM6104307" "Reanalyzed by: GSM6104300" "Reanalyzed by: GSM6104260" "Reanalyzed by: GSM6104757" "Reanalyzed by: GSM6104869" "Reanalyzed by... |
!Sample_relation "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06556981" "" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06557055" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06556953" "BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06557008" "BioSample: https://www.ncbi.nlm.nih.gov... |
!Sample_supplementary_file_1 "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NONE" "NON... |
!series_matrix_table_begin |
"ID_REF" "GSM2528085" "GSM2528086" "GSM2528220" "GSM2528263" "GSM2528297" "GSM2528305" "GSM2528307" "GSM2528320" "GSM2528324" "GSM2528325" "GSM2528341" "GSM2528345" "GSM2528347" "GSM2528349" "GSM2528365" "GSM2528392" "GSM2528404" "GSM2528410" "GSM2528419" "GSM2528433" "GSM2528437" "GSM2528439" "GSM2528441" "GSM2528449"... |
!series_matrix_table_end |
Gene panels for this study can be found here: https://github.com/cBioPortal/datahub/tree/master/reference_data/gene_panels |
cancer_study_identifier: brca_metabric |
stable_id: brca_metabric_all |
case_list_name: All samples |
case_list_description: All samples (2509 samples) |
case_list_category: all_cases_in_study |
case_list_ids: MB-5489 MB-5482 MB-5483 MB-5481 MB-5486 MB-5484 MB-5485 MB-7212 MB-5648 MB-5645 MB-5646 MB-5647 MB-5640 MB-5641 MB-5642 MTS-T2068 MB-7217 MB-3429 MB-6359 MB-6358 MTS-T2064 MTS-T2065 MTS-T2066 MB-0238 MB-0239 MB-0236 MB-0234 MB-0235 MB-0232 MB-0233 MB-0230 MB-0231 MB-6179 MB-6178 MB-4849 MB-4845 MB-6171 M... |
cancer_study_identifier: brca_metabric |
stable_id: brca_metabric_cna |
case_list_name: Samples with CNA data |
case_list_description: Samples with CNA data (2173 samples) |
case_list_category: all_cases_with_cna_data |
case_list_ids: MB-5489 MB-5482 MB-5483 MB-5481 MB-5486 MB-5484 MB-5485 MB-5648 MB-5645 MB-5646 MB-5647 MB-5640 MB-5641 MB-5642 MB-3429 MB-6359 MB-6358 MB-0238 MB-0239 MB-0236 MB-0234 MB-0235 MB-0232 MB-0233 MB-0230 MB-0231 MB-6179 MB-6178 MB-4849 MB-4845 MB-6171 MB-4846 MB-4843 MB-3526 MB-3525 MB-3528 MTS-T2398 MTS-T23... |
cancer_study_identifier: brca_metabric |
stable_id: brca_metabric_cnaseq |
case_list_name: Samples with mutation and CNA data |
case_list_description: Samples with mutation and CNA data (2051 samples) |
case_list_category: all_cases_with_mutation_and_cna_data |
case_list_ids: MB-5489 MB-5482 MB-5483 MB-5481 MB-5486 MB-5484 MB-5485 MB-5645 MB-5646 MB-5647 MB-5640 MB-5641 MB-5642 MB-3429 MB-6359 MB-6358 MB-0238 MB-0239 MB-0236 MB-0234 MB-0235 MB-0232 MB-0233 MB-0230 MB-0231 MB-6179 MB-6178 MB-4849 MB-4845 MB-6171 MB-4846 MB-4843 MB-3526 MB-3525 MB-3528 MTS-T2398 MTS-T2392 MTS-T... |
cancer_study_identifier: brca_metabric |
stable_id: brca_metabric_3way_complete |
case_list_name: Complete samples |
case_list_description: Samples with mutation, CNA and expression data (1866 samples) |
case_list_category: all_cases_with_mutation_and_cna_and_mrna_data |
case_list_ids: MB-5489 MB-5482 MB-5483 MB-5481 MB-5486 MB-5484 MB-5485 MB-5645 MB-5646 MB-5647 MB-5640 MB-5641 MB-5642 MB-3429 MB-6359 MB-6358 MB-0238 MB-0239 MB-0236 MB-0234 MB-0235 MB-0232 MB-0233 MB-0230 MB-0231 MB-6179 MB-6178 MB-4849 MB-4845 MB-6171 MB-4846 MB-4843 MB-3526 MB-3525 MB-3528 MB-6007 MB-6006 MB-6001 M... |
cancer_study_identifier: brca_metabric |
stable_id: brca_metabric_mrna |
case_list_name: Samples with mRNA data (Illumina Human v3 microarray) |
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