Datasets:

chumphati
/

Atlantis_Human_SRA_RNA-seq_Metadata_Atlas

Error code:   DatasetGenerationError
Exception:    ArrowInvalid
Message:      Failed to parse string: 'unknown' as a scalar of type int64
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1856, in _prepare_split_single
                  writer.write_table(table)
                  ~~~~~~~~~~~~~~~~~~^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 811, in write_table
                  self._write_table(pa_table, writer_batch_size=writer_batch_size)
                  ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 822, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2381, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2315, in cast_table_to_schema
                  cast_array_to_feature(
                  ~~~~~~~~~~~~~~~~~~~~~^
                      table[name] if name in table_column_names else pa.array([None] * len(table), type=schema.field(name).type),
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                      feature,
                      ^^^^^^^^
                  )
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1861, in wrapper
                  return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
                                           ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2155, in cast_array_to_feature
                  return array_cast(
                      array,
                  ...<2 lines>...
                      allow_decimal_to_str=allow_decimal_to_str,
                  )
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 1863, in wrapper
                  return func(array, *args, **kwargs)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2015, in array_cast
                  return array.cast(pa_type)
                         ~~~~~~~~~~^^^^^^^^^
                File "pyarrow/array.pxi", line 1186, in pyarrow.lib.Array.cast
                File "/usr/local/lib/python3.14/site-packages/pyarrow/compute.py", line 414, in cast
                  return call_function("cast", [arr], options, memory_pool)
                File "pyarrow/_compute.pyx", line 604, in pyarrow._compute.call_function
                  return func.call(args, options=options, memory_pool=memory_pool,
                File "pyarrow/_compute.pyx", line 399, in pyarrow._compute.Function.call
                  result = GetResultValue(
                File "pyarrow/error.pxi", line 155, in pyarrow.lib.pyarrow_internal_check_status
                  return check_status(status)
                File "pyarrow/error.pxi", line 92, in pyarrow.lib.check_status
                  raise convert_status(status)
              pyarrow.lib.ArrowInvalid: Failed to parse string: 'unknown' as a scalar of type int64
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1379, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~^
                      builder, max_dataset_size_bytes=max_dataset_size_bytes
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 956, in stream_convert_to_parquet
                  builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
                  ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1702, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~^
                      gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  ):
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1887, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset

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run_accession string	study_accession string	instrument_platform string	library_selection string	library_strategy string	base_count int64	sequencing_source string	biopsy_site string	bs_uberon_code string	biopsy_type string	cell_line string	cellosaurus_code string	cell_type string	cl_code string	organ string	organ_uberon_code string	disease string	do_code string	is_cancer bool	treatment string	treatment_time string	response string	age string	sex string	ethnicity string	conf_organ_1_5 float64	conf_biopsy_site_1_5 float64	conf_cell_type_1_5 float64	conf_cell_line_1_5 float64	conf_disease_1_5 float64	conf_is_cancer_1_5 int64	conf_sex_1_5 float64	conf_age_1_5 float64	conf_biopsy_type_1_5 int64	conf_ethnicity_1_5 float64	conf_treatment_1_5 float64	conf_treatment_time_1_5 null	conf_response_1_5 null	conf_sequencing_source_1_5 int64	conf_organ_uberon_code_1_5 float64	conf_bs_uberon_code_1_5 float64	conf_cl_code_1_5 float64	conf_do_code_1_5 float64	conf_cellosaurus_code_1_5 float64	row_confidence_1_5 int64	confidence_flags string
DRR000897	PRJDA63201	ILLUMINA	other	RNA-Seq	837,507,136	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	unknown	not applicable	not applicable	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	null	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex)
DRR001173	PRJDA69989	ILLUMINA	other	RNA-Seq	942,609,312	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell	CL:0001064	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	25 mm	unknown	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment)
DRR001174	PRJDA69989	ILLUMINA	other	RNA-Seq	1,683,594,408	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell	CL:0001064	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	25 mm	unknown	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment)
DRR001175	PRJDA69989	ILLUMINA	other	RNA-Seq	1,274,794,436	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell; epithelial cell	CL:0001064; CL:0000066	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	unknown	not applicable	not applicable	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	null	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex)
DRR001176	PRJDA69989	ILLUMINA	other	RNA-Seq	1,068,884,424	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell	CL:0001064	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	unknown	not applicable	not applicable	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	null	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex)
DRR001622	PRJDA74549	ILLUMINA	other	RNA-Seq	2,198,179,768	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001624	PRJDA74549	ILLUMINA	other	RNA-Seq	2,233,820,728	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001627	PRJDA74549	ILLUMINA	other	RNA-Seq	1,997,235,160	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001628	PRJDA74549	ILLUMINA	other	RNA-Seq	14,192,528,648	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001629	PRJDA74549	ILLUMINA	other	RNA-Seq	9,786,770,344	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001630	PRJDA74549	ILLUMINA	other	RNA-Seq	8,876,218,904	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001631	PRJDA74549	ILLUMINA	other	RNA-Seq	7,762,199,960	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001632	PRJDA74549	ILLUMINA	other	RNA-Seq	12,043,796,912	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001633	PRJDA74549	ILLUMINA	other	RNA-Seq	6,548,106,344	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001634	PRJDA74549	ILLUMINA	other	RNA-Seq	7,532,415,936	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001635	PRJDA74549	ILLUMINA	other	RNA-Seq	7,681,848,200	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001636	PRJDA74549	ILLUMINA	other	RNA-Seq	10,748,726,512	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001637	PRJDA74549	ILLUMINA	other	RNA-Seq	9,256,447,208	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001638	PRJDA74549	ILLUMINA	other	RNA-Seq	7,664,614,440	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001639	PRJDA74549	ILLUMINA	other	RNA-Seq	9,034,120,608	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001640	PRJDA74549	ILLUMINA	other	RNA-Seq	6,413,906,608	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001641	PRJDA74549	ILLUMINA	other	RNA-Seq	5,890,259,464	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001642	PRJDA74549	ILLUMINA	other	RNA-Seq	6,590,409,312	bulk	brain	UBERON:0000955	primary	primary tissue	unknown	unknown	unknown	brain	UBERON:0000955	unknown	unknown	false	unknown	not applicable	not applicable	unknown	male	unknown	4	4	null	4	null	3	3	null	4	null	null	null	null	3	4	4	null	null	null	3	INFO:EVIDENCE_NOT_CORROBORATED(is_cancer,sequencing_source,sex)
DRR001796	PRJDB2001	ILLUMINA	polyA	RNA-Seq	19,871,719,000	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	unknown	not applicable	not applicable	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	null	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex)
DRR001797	PRJDB2001	ILLUMINA	polyA	RNA-Seq	19,708,528,806	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	transduced	unknown	unknown	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	3	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex,treatment)
DRR001798	PRJDB2001	ILLUMINA	polyA	RNA-Seq	19,612,387,594	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	unknown	not applicable	not applicable	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	null	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex)
DRR001799	PRJDB2001	ILLUMINA	polyA	RNA-Seq	19,548,965,270	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	s34f	unknown	unknown	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	3	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex,treatment)
DRR002271	PRJDB2542	ILLUMINA	polyA	RNA-Seq	1,493,774,964	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	unknown	not applicable	not applicable	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	null	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex)
DRR002272	PRJDB2542	ILLUMINA	polyA	RNA-Seq	1,334,053,656	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	unknown	not applicable	not applicable	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	null	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex)
DRR002273	PRJDB2542	ILLUMINA	polyA	RNA-Seq	1,389,093,876	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	unknown	not applicable	not applicable	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	null	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex)
DRR002274	PRJDB2542	ILLUMINA	polyA	RNA-Seq	1,207,290,528	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	siupf1	unknown	unknown	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	3	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex,treatment)
DRR002275	PRJDB2542	ILLUMINA	polyA	RNA-Seq	1,596,190,284	bulk	uterus; cervix epithelium	UBERON:0000995; UBERON:0004801	primary	HeLa	CVCL_0030	unknown	unknown	uterine cervix	UBERON:0000002	human papillomavirus-related endocervical adenocarcinoma	unknown	true	siupf1	unknown	unknown	30Y6MO	female	african american	4	4	null	4	3	3	3	3	3	3	3	null	null	3	4	4	null	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,disease,ethnicity,is_cancer,sequencing_source,sex,treatment)
DRR002593	PRJDB2198	ILLUMINA	other	RNA-Seq	1,501,885,400	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell; epithelial cell	CL:0001064; CL:0000066	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	glucose deprivation	3h	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment,treatment_time)
DRR002594	PRJDB2198	ILLUMINA	other	RNA-Seq	1,294,879,374	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell; epithelial cell	CL:0001064; CL:0000066	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	glucose deprivation	3h	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment,treatment_time)
DRR002595	PRJDB2198	ILLUMINA	other	RNA-Seq	1,738,426,052	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell; epithelial cell	CL:0001064; CL:0000066	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	glucose deprivation	6h	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment,treatment_time)
DRR002596	PRJDB2198	ILLUMINA	other	RNA-Seq	1,155,046,632	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell; epithelial cell	CL:0001064; CL:0000066	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	glucose deprivation	6h	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment,treatment_time)
DRR002597	PRJDB2198	ILLUMINA	other	RNA-Seq	1,464,629,288	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell; epithelial cell	CL:0001064; CL:0000066	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	glucose deprivation	9h	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment,treatment_time)
DRR002598	PRJDB2198	ILLUMINA	other	RNA-Seq	2,157,903,378	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell; epithelial cell	CL:0001064; CL:0000066	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	glucose deprivation	9h	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment,treatment_time)
DRR002599	PRJDB2198	ILLUMINA	other	RNA-Seq	2,377,391,530	bulk	urinary bladder	UBERON:0001255	primary	T24	CVCL_0554	malignant cell; epithelial cell	CL:0001064; CL:0000066	urinary bladder	UBERON:0001255	urinary bladder cancer	DOID:11054	true	glucose deprivation	24h	unknown	82Y	female	caucasian	4	4	4	4	4	4	3	3	3	3	3	null	null	3	4	4	4	4	4	4	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,ethnicity,sequencing_source,sex,treatment,treatment_time)
DRR003595	PRJDB2065	ILLUMINA	other	RNA-Seq	1,661,020,003	bulk	eye; retina; pigmented layer of retina	UBERON:0000970; UBERON:0000966; UBERON:0001782	primary	hTERT-RPE1	CVCL_4388	retinal pigment epithelial cell	CL:0002586	unknown	unknown	unknown	unknown	false	control sirna	unknown	unknown	1Y	female	unknown	null	4	4	4	null	3	3	3	3	null	3	null	null	3	null	4	4	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,is_cancer,sequencing_source,sex,treatment)
DRR003596	PRJDB2065	ILLUMINA	other	RNA-Seq	1,693,351,824	bulk	eye; retina; pigmented layer of retina	UBERON:0000970; UBERON:0000966; UBERON:0001782	primary	hTERT-RPE1	CVCL_4388	retinal pigment epithelial cell	CL:0002586	unknown	unknown	unknown	unknown	false	hbix1 sirna	unknown	unknown	1Y	female	unknown	null	4	4	4	null	3	3	3	3	null	3	null	null	3	null	4	4	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,is_cancer,sequencing_source,sex,treatment)
DRR003597	PRJDB2065	ILLUMINA	other	RNA-Seq	1,575,019,797	bulk	eye; retina; pigmented layer of retina	UBERON:0000970; UBERON:0000966; UBERON:0001782	primary	hTERT-RPE1	CVCL_4388	retinal pigment epithelial cell	CL:0002586	unknown	unknown	unknown	unknown	false	sirna	unknown	unknown	1Y	female	unknown	null	4	4	4	null	3	3	3	3	null	3	null	null	3	null	4	4	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,is_cancer,sequencing_source,sex,treatment)
DRR003598	PRJDB2065	ILLUMINA	other	RNA-Seq	917,636,211	bulk	eye; retina; pigmented layer of retina	UBERON:0000970; UBERON:0000966; UBERON:0001782	primary	hTERT-RPE1	CVCL_4388	retinal pigment epithelial cell	CL:0002586	unknown	unknown	unknown	unknown	false	xist sirna	unknown	unknown	1Y	female	unknown	null	4	4	4	null	3	3	3	3	null	3	null	null	3	null	4	4	null	4	3	INFO:EVIDENCE_NOT_CORROBORATED(age,biopsy_type,is_cancer,sequencing_source,sex,treatment)
DRR006374	PRJDB2573	ILLUMINA	other	RNA-Seq	904,787,892	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	rna-pcr	unknown	unknown	unknown	unknown	indonesia	4	4	null	3	4	3	null	null	4	3	3	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,treatment)
DRR006375	PRJDB2573	ILLUMINA	other	RNA-Seq	969,379,956	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	rna	unknown	unknown	unknown	unknown	indonesia	4	4	null	3	4	3	null	null	4	3	3	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,treatment)
DRR006376	PRJDB2573	ILLUMINA	other	RNA-Seq	1,018,550,772	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	rna	unknown	unknown	unknown	unknown	indonesia	4	4	null	3	4	3	null	null	4	3	3	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,treatment)
DRR006377	PRJDB2573	ILLUMINA	other	RNA-Seq	919,252,188	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	rna	unknown	unknown	unknown	unknown	indonesia	4	4	null	3	4	3	null	null	4	3	3	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,treatment)
DRR006378	PRJDB2573	ILLUMINA	other	RNA-Seq	802,376,568	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	rna	unknown	unknown	unknown	unknown	indonesia	4	4	null	3	4	3	null	null	4	3	3	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,treatment)
DRR006379	PRJDB2573	ILLUMINA	other	RNA-Seq	1,155,551,472	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	rna-pcr	unknown	unknown	unknown	unknown	indonesia	4	4	null	3	4	3	null	null	4	3	3	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,treatment)
DRR006380	PRJDB2573	ILLUMINA	other	RNA-Seq	1,095,352,704	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	rna	unknown	unknown	unknown	male	indonesia:manado	4	4	null	3	4	3	5	null	4	3	3	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,treatment)
DRR006381	PRJDB2573	ILLUMINA	other	RNA-Seq	1,405,230,264	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006382	PRJDB2573	ILLUMINA	other	RNA-Seq	1,310,010,768	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	rna	unknown	unknown	unknown	female	indonesia:manado	4	4	null	3	4	3	5	null	4	3	3	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,treatment)
DRR006383	PRJDB2573	ILLUMINA	other	RNA-Seq	1,362,454,956	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006384	PRJDB2573	ILLUMINA	other	RNA-Seq	1,161,191,808	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006385	PRJDB2573	ILLUMINA	other	RNA-Seq	1,205,176,140	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006386	PRJDB2573	ILLUMINA	other	RNA-Seq	1,263,890,880	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia	4	4	null	3	4	3	3	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source,sex)
DRR006387	PRJDB2573	ILLUMINA	other	RNA-Seq	1,343,810,808	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006388	PRJDB2573	ILLUMINA	other	RNA-Seq	1,260,349,812	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006389	PRJDB2573	ILLUMINA	other	RNA-Seq	3,995,018,712	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006390	PRJDB2573	ILLUMINA	other	RNA-Seq	4,152,753,036	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006391	PRJDB2573	ILLUMINA	other	RNA-Seq	1,354,060,728	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006392	PRJDB2573	ILLUMINA	other	RNA-Seq	1,396,152,720	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006393	PRJDB2573	ILLUMINA	other	RNA-Seq	1,352,147,904	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006394	PRJDB2573	ILLUMINA	other	RNA-Seq	1,219,565,088	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006395	PRJDB2573	ILLUMINA	other	RNA-Seq	3,401,654,148	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006396	PRJDB2573	ILLUMINA	other	RNA-Seq	1,168,000,200	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006397	PRJDB2573	ILLUMINA	other	RNA-Seq	1,390,483,548	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006398	PRJDB2573	ILLUMINA	other	RNA-Seq	1,438,045,920	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006399	PRJDB2573	ILLUMINA	other	RNA-Seq	1,425,104,892	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006400	PRJDB2573	ILLUMINA	other	RNA-Seq	1,352,658,060	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006401	PRJDB2573	ILLUMINA	other	RNA-Seq	3,685,741,344	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006402	PRJDB2573	ILLUMINA	other	RNA-Seq	670,000,536	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006403	PRJDB2573	ILLUMINA	other	RNA-Seq	1,756,793,412	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006404	PRJDB2573	ILLUMINA	other	RNA-Seq	1,354,154,328	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006405	PRJDB2573	ILLUMINA	other	RNA-Seq	1,280,803,608	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006406	PRJDB2573	ILLUMINA	other	RNA-Seq	800,501,796	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006407	PRJDB2573	ILLUMINA	other	RNA-Seq	1,215,038,880	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006408	PRJDB2573	ILLUMINA	other	RNA-Seq	794,213,424	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006409	PRJDB2573	ILLUMINA	other	RNA-Seq	618,784,272	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006410	PRJDB2573	ILLUMINA	other	RNA-Seq	799,444,836	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006411	PRJDB2573	ILLUMINA	other	RNA-Seq	892,184,688	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006412	PRJDB2573	ILLUMINA	other	RNA-Seq	1,114,844,544	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006413	PRJDB2573	ILLUMINA	other	RNA-Seq	1,384,376,904	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006414	PRJDB2573	ILLUMINA	other	RNA-Seq	1,168,161,768	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006415	PRJDB2573	ILLUMINA	other	RNA-Seq	1,171,413,360	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006416	PRJDB2573	ILLUMINA	other	RNA-Seq	1,092,049,884	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006417	PRJDB2573	ILLUMINA	other	RNA-Seq	1,293,147,648	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006418	PRJDB2573	ILLUMINA	other	RNA-Seq	1,307,210,040	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006419	PRJDB2573	ILLUMINA	other	RNA-Seq	1,275,646,032	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006420	PRJDB2573	ILLUMINA	other	RNA-Seq	1,395,470,664	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006421	PRJDB2573	ILLUMINA	other	RNA-Seq	1,330,920,828	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006422	PRJDB2573	ILLUMINA	other	RNA-Seq	1,378,854,936	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006423	PRJDB2573	ILLUMINA	other	RNA-Seq	1,447,009,704	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006424	PRJDB2573	ILLUMINA	other	RNA-Seq	1,235,755,368	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006425	PRJDB2573	ILLUMINA	other	RNA-Seq	1,225,777,680	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006426	PRJDB2573	ILLUMINA	other	RNA-Seq	1,551,120,876	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006427	PRJDB2573	ILLUMINA	other	RNA-Seq	3,247,644,768	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:manado	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006428	PRJDB2573	ILLUMINA	other	RNA-Seq	1,333,974,348	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006429	PRJDB2573	ILLUMINA	other	RNA-Seq	1,365,948,612	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	male	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)
DRR006430	PRJDB2573	ILLUMINA	other	RNA-Seq	1,501,837,488	bulk	blood	UBERON:0000178	blood	primary tissue	unknown	unknown	unknown	blood	UBERON:0000178	malaria	DOID:12365	false	unknown	not applicable	not applicable	unknown	female	indonesia:bitung	4	4	null	3	4	3	5	null	4	3	null	null	null	3	4	4	null	4	null	4	INFO:EVIDENCE_NOT_CORROBORATED(cell_line,ethnicity,is_cancer,sequencing_source)

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Atlantis Human SRA RNA-seq Metadata Atlas (2012–2025)

Overview

This dataset contains standardized metadata for 1 037 214 human RNA-seq runs from 49 246 SRA studies published between 2012 and 2025. Each row represents one unique run_accession. The dataset combines run-, study- and sample-level information collected from SRA/ENA and BioSample records, followed by metadata reconstruction, normalization and biological ontology mapping.

All samples were annotated with Metappuccino (Fiona Hak, Camille Marchet, Daniel Gautheret, Mélina Gallopin, Metappuccino: large language model-driven reconstruction of sequence read archive metadata for cancer research, Bioinformatics, Volume 42, Issue 5, May 2026, btag166, https://doi.org/10.1093/bioinformatics/btag166).

The resulting table provides harmonized descriptions of the sequencing protocol, biological material, anatomical origin, disease status, treatment and donor characteristics. It is intended to support large-scale RNA-seq dataset discovery, filtering, quality assessment and construction of biologically defined subsets.

Main file

1M_2012-2025_rnaseq_SRA_metadata_v1126.csv.gz

The file contains:

over 1 million unique RNA-seq runs
49 246 unique studies
one row per run_accession

Dataset construction

Human RNA-seq records published between 2012 and 2025 were collected from public SRA/ENA metadata. Information distributed across run, study and BioSample records was consolidated at the run level. Metadata values were then cleaned and normalized to reduce differences in spelling, formatting and terminology across studies.

Biological annotations include standardized biopsy sites, organs, cell lines, cell types, diseases, treatments and donor attributes. Anatomical terms were mapped to UBERON, cell types to the Cell Ontology, and diseases to the Disease Ontology whenever a sufficiently reliable mapping was available. Cell-line annotations were additionally standardized using Cellosaurus.

The dataset includes bulk, single-cell and spatial RNA-seq experiments. Single-cell samples were further classified as droplet-like, plate-like or unknown when the available protocol metadata allowed this distinction.

No biological subset is imposed in the main file. Healthy and diseased samples, primary tissues and cell lines, cancer and non-cancer samples, and different RNA-selection protocols are retained.

Metadata fields

The principal metadata fields are:

run_accession: unique SRA run identifier
study_accession: associated study or project identifier
instrument_platform: sequencing platform
library_selection: normalized RNA-selection protocol
library_strategy: sequencing strategy
base_count: number of sequenced bases
sequencing_source: bulk, spatial or single-cell protocol category
biopsy_site: anatomical sampling location
bs_uberon_code: UBERON identifier for the biopsy site
biopsy_type: type of biological sample
cell_line: standardized cell-line annotation or primary-tissue status
cell_type: standardized cell-type annotation
cl_code: Cell Ontology identifier
organ: standardized organ annotation
organ_uberon_code: UBERON identifier for the organ
disease: standardized disease or health status
do_code: Disease Ontology identifier
is_cancer: normalized cancer-status indicator
treatment: treatment or experimental exposure
treatment_time: reported treatment duration
response: reported biological or clinical response
age: normalized donor age
sex: normalized donor sex
ethnicity: normalized donor ethnicity

Confidence scores

Each reconstructed biological annotation is assigned a heuristic confidence score from 1 to 5 (conf_<field>_1_5), based on supporting evidence from the original SRA metadata, biological reference databases, ontologies, and consistency checks. A separate row_confidence_1_5 score assesses the overall reliability of the sample annotations, taking into account the available evidence and detected inconsistencies rather than averaging individual scores. The confidence_flags column identifies potential inconsistencies and annotations requiring further review. These scores are intended to help to assess and filter metadata, not to represent statistical probabilities of correctness. Detailed scoring criteria and flag definitions are available in confidence_score/.

Missing values

Missing, unavailable or insufficiently supported metadata are represented by unknown. An unknown value does not necessarily indicate that the information was absent from every original database record; it may also indicate that the available information could not be mapped or inferred with sufficient reliability.

Ontology codes may also remain unknown when the corresponding biological annotation could not be mapped unambiguously.

Limitations

The dataset is derived from public metadata and therefore depends on the completeness and accuracy of the original SRA, ENA and BioSample records. Some annotations were reconstructed from free-text descriptions and may remain uncertain despite normalization and confidence scoring. Multiple runs may originate from the same biological sample, donor or experimental condition, and a unique run_accession should not automatically be interpreted as an independent biological replicate.

The confidence system evaluates metadata reliability and biological consistency but does not assess sequencing-read quality, RNA integrity, batch effects or suitability for a specific downstream analysis.

Version

Last version: v1126

Cite

Fiona Hak, Camille Marchet, Daniel Gautheret, Mélina Gallopin, Atlantis Human SRA RNA-seq Metadata Atlas (2012–2025), 10.5281/zenodo.23987427, https://huggingface.co/datasets/chumphati/1M_RNAseq_SRA_samples_annotations/tree/main

Fiona Hak, Camille Marchet, Daniel Gautheret, Mélina Gallopin, Metappuccino: large language model-driven reconstruction of sequence read archive metadata for cancer research, Bioinformatics, Volume 42, Issue 5, May 2026, btag166, https://doi.org/10.1093/bioinformatics/btag166

This project was provided with computing HPC and storage resources by GENCI at IDRIS thanks to the grant 2025-A0210316710 on the supercomputer Jean Zay's A100 partition.

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