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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 9 new columns ({'Other seq', '3D seq', 'Published?', 'Median QC score', 'Protocols', 'ChIP-seq', 'ATAC-seq', 'RNA-seq', 'Organisms'}) and 8 missing columns ({'Sample name', 'Read depth', 'Treatment', 'QC score', 'Replicate', 'Protocol', 'Cell type', 'Organism'}).
This happened while the csv dataset builder was generating data using
hf://datasets/funlab/DBNascent/datasets.csv (at revision 2b150727f77de6fa2e9f105d664e2ff4e69efa38)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2011, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, in write_table
pa_table = table_cast(pa_table, self._schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2302, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2256, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
Paper identifier: string
Protocols: string
Organisms: string
Published?: string
Median QC score: double
ATAC-seq: string
RNA-seq: string
ChIP-seq: string
3D seq: string
Other seq: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1456
to
{'Sample name': Value(dtype='string', id=None), 'Paper identifier': Value(dtype='string', id=None), 'Organism': Value(dtype='string', id=None), 'Protocol': Value(dtype='string', id=None), 'Cell type': Value(dtype='string', id=None), 'Treatment': Value(dtype='string', id=None), 'Replicate': Value(dtype='int64', id=None), 'Read depth': Value(dtype='string', id=None), 'QC score': Value(dtype='int64', id=None)}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1577, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1191, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1882, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2013, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 9 new columns ({'Other seq', '3D seq', 'Published?', 'Median QC score', 'Protocols', 'ChIP-seq', 'ATAC-seq', 'RNA-seq', 'Organisms'}) and 8 missing columns ({'Sample name', 'Read depth', 'Treatment', 'QC score', 'Replicate', 'Protocol', 'Cell type', 'Organism'}).
This happened while the csv dataset builder was generating data using
hf://datasets/funlab/DBNascent/datasets.csv (at revision 2b150727f77de6fa2e9f105d664e2ff4e69efa38)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Sample name
string | Paper identifier
string | Organism
string | Protocol
string | Cell type
string | Treatment
string | Replicate
int64 | Read depth
string | QC score
int64 |
|---|---|---|---|---|---|---|---|---|
ERR769522
|
Laitem2015cdk9
|
H. sapiens
|
GRO-seq
|
HeLa (cell line)
|
DRB (30min)
| 1
|
20M
| 4
|
ERR769523
|
Laitem2015cdk9
|
H. sapiens
|
GRO-seq
|
HeLa (cell line)
|
KM05283 (30min)
| 1
|
23M
| 4
|
ERR769524
|
Laitem2015cdk9
|
H. sapiens
|
GRO-seq
|
HeLa (cell line)
| null | 1
|
24M
| 2
|
ERR769525
|
Laitem2015cdk9
|
H. sapiens
|
GRO-seq
|
HeLa (cell line)
| null | 2
|
26M
| 2
|
SRM497904
|
Hah2013enhancer
|
H. sapiens
|
GRO-seq
|
MCF7 (cell line)
|
ethanol
| 1
|
40M
| 3
|
SRM497907
|
Hah2013enhancer
|
H. sapiens
|
GRO-seq
|
MCF7 (cell line)
|
ethanol
| 2
|
49M
| 2
|
SRM497911
|
Hah2013enhancer
|
H. sapiens
|
GRO-seq
|
MCF7 (cell line)
|
17-beta-estradiol (10min)
| 1
|
41M
| 2
|
SRM497912
|
Hah2013enhancer
|
H. sapiens
|
GRO-seq
|
MCF7 (cell line)
|
17-beta-estradiol (10min)
| 2
|
52M
| 3
|
SRM497914
|
Hah2013enhancer
|
H. sapiens
|
GRO-seq
|
MCF7 (cell line)
|
17-beta-estradiol (40min)
| 1
|
46M
| 2
|
SRM497917
|
Hah2013enhancer
|
H. sapiens
|
GRO-seq
|
MCF7 (cell line)
|
17-beta-estradiol (40min)
| 2
|
38M
| 2
|
SRR064994
|
Core2012defining
|
D. melanogaster
|
GRO-seq
|
S2 (cell line)
| null | 1
|
6M
| 4
|
SRR065240
|
Escoubet-lozach2011mechanisms
|
M. musculus
|
GRO-seq
|
peritoneal macrophage (primary)
|
DMSO (1hr)
| 1
|
8M
| 4
|
SRR065241
|
Escoubet-lozach2011mechanisms
|
M. musculus
|
GRO-seq
|
peritoneal macrophage (primary)
|
Kdo2-Lipid A (1hr)
| 1
|
8M
| 4
|
SRR073010
|
Larschan2011x
|
D. melanogaster
|
GRO-seq
|
S2 (cell line)
| null | 2
|
11M
| 4
|
SRR091798
|
Ji2011transcriptional
|
M. musculus
|
GRO-seq
|
C2C12 (cell line)
| null | 1
|
17M
| 2
|
SRR097862
|
Min2011regulating
|
M. musculus
|
GRO-seq
|
ESC (cell line)
| null | 3
|
8M
| 4
|
SRR097863
|
Min2011regulating
|
M. musculus
|
GRO-seq
|
MEF (primary)
| null | 1
|
8M
| 4
|
SRR097864
|
Min2011regulating
|
M. musculus
|
GRO-seq
|
MEF (primary)
| null | 2
|
7M
| 4
|
SRR10063517
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HAEC (primary)
|
growth media (6hr)
| 1
|
19M
| 2
|
SRR10063518
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HAEC (primary)
|
growth media (6hr)
| 2
|
9M
| 4
|
SRR10063519
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HAEC (primary)
|
hypoxia (6hr)
| 1
|
18M
| 2
|
SRR10063520
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HAEC (primary)
|
hypoxia (6hr)
| 2
|
8M
| 4
|
SRR10063521
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HAEC (primary)
|
oxPAPC (6hr)
| 1
|
15M
| 3
|
SRR10063522
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HAEC (primary)
|
oxPAPC (6hr)
| 2
|
11M
| 3
|
SRR10063523
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HAEC (primary)
|
hypoxia (6hr) , oxPAPC (6hr)
| 1
|
16M
| 2
|
SRR10063524
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HAEC (primary)
|
hypoxia (6hr) , oxPAPC (6hr)
| 2
|
16M
| 2
|
SRR10063525
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
growth media (6hr)
| 1
|
19M
| 2
|
SRR10063526
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
growth media (6hr)
| 2
|
15M
| 2
|
SRR10063527
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
hypoxia (6hr)
| 1
|
15M
| 3
|
SRR10063528
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
hypoxia (6hr)
| 2
|
17M
| 2
|
SRR10063529
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
hypoxia (6hr)
| 3
|
13M
| 3
|
SRR10063530
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
oxPAPC (6hr)
| 1
|
99M
| 4
|
SRR10063531
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
oxPAPC (6hr)
| 2
|
14M
| 3
|
SRR10063532
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
oxPAPC (6hr)
| 3
|
12M
| 3
|
SRR10063533
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
hypoxia (6hr) , oxPAPC (6hr)
| 1
|
51M
| 4
|
SRR10063534
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
hypoxia (6hr) , oxPAPC (6hr)
| 2
|
16M
| 2
|
SRR10063535
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HUVEC (primary)
|
hypoxia (6hr) , oxPAPC (6hr)
| 3
|
14M
| 3
|
SRR10063536
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HASM (primary)
|
growth media (6hr)
| 1
|
14M
| 3
|
SRR10063537
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HASM (primary)
|
growth media (6hr)
| 2
|
23M
| 2
|
SRR10063540
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HASM (primary)
|
oxPAPC (6hr)
| 1
|
17M
| 2
|
SRR10063541
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
HASM (primary)
|
oxPAPC (6hr)
| 2
|
7M
| 4
|
SRR10063544
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
CD14+ macrophage (primary)
|
growth media (6hr)
| 1
|
19M
| 2
|
SRR10063545
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
CD14+ macrophage (primary)
|
growth media (6hr)
| 2
|
26M
| 2
|
SRR10063548
|
Linnakuosmanen2020nrf2
|
H. sapiens
|
GRO-seq
|
CD14+ macrophage (primary)
|
oxPAPC (6hr)
| 1
|
18M
| 2
|
SRR10067473
|
Kelly2020unpublished
|
M. musculus
|
PRO-seq
|
ESC (cell line)
| null | 1
|
41M
| 2
|
SRR10067474
|
Kelly2020unpublished
|
M. musculus
|
PRO-seq
|
ESC (cell line)
| null | 2
|
23M
| 1
|
SRR10067475
|
Kelly2020unpublished
|
M. musculus
|
PRO-seq
|
ESC (cell line)
|
JQ1 (2hr)
| 1
|
29M
| 2
|
SRR10067476
|
Kelly2020unpublished
|
M. musculus
|
PRO-seq
|
ESC (cell line)
|
JQ1 (2hr)
| 2
|
15M
| 2
|
SRR10067477
|
Kelly2020unpublished
|
M. musculus
|
PRO-seq
|
ESC (cell line)
|
LBH589 (2hr)
| 1
|
51M
| 2
|
SRR10067478
|
Kelly2020unpublished
|
M. musculus
|
PRO-seq
|
ESC (cell line)
|
LBH589 (2hr)
| 2
|
10M
| 3
|
SRR10067479
|
Kelly2020unpublished
|
M. musculus
|
PRO-seq
|
ESC (cell line)
|
LBH589 (6hr)
| 1
|
30M
| 1
|
SRR10067480
|
Kelly2020unpublished
|
M. musculus
|
PRO-seq
|
ESC (cell line)
|
LBH589 (6hr)
| 2
|
42M
| 2
|
SRR1015583
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
| null | 1
|
22M
| 1
|
SRR1015584
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
| null | 2
|
23M
| 1
|
SRR1015585
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
|
TNF-alpha (10min)
| 1
|
21M
| 1
|
SRR1015586
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
|
TNF-alpha (10min)
| 2
|
18M
| 2
|
SRR1015587
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
|
TNF-alpha (30min)
| 1
|
16M
| 2
|
SRR1015588
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
|
TNF-alpha (30min)
| 2
|
21M
| 1
|
SRR1015589
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
|
TNF-alpha (2hr)
| 1
|
20M
| 2
|
SRR1015590
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
|
TNF-alpha (2hr)
| 2
|
24M
| 1
|
SRR1015591
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
|
DMSO (15min)
| 1
|
77M
| 1
|
SRR1015592
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
|
DMSO (15min)
| 2
|
55M
| 1
|
SRR1015593
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
| null | 1
|
130M
| 3
|
SRR1015594
|
Luo2014dynamic
|
H. sapiens
|
GRO-seq
|
AC16 (cell line)
| null | 2
|
154M
| 4
|
SRR10282967
|
Komarov2020epigenetic
|
D. melanogaster
|
GRO-seq
|
ovary (tissue)
| null | 1
|
25M
| 3
|
SRR10282968
|
Komarov2020epigenetic
|
D. melanogaster
|
GRO-seq
|
ovary (tissue)
| null | 1
|
23M
| 3
|
SRR10298307
|
Li2021comprehensive
|
H. sapiens
|
GRO-seq
|
MCF7 (cell line)
| null | 1
|
64M
| 2
|
SRR10298308
|
Li2021comprehensive
|
H. sapiens
|
GRO-seq
|
MCF7 (cell line)
| null | 2
|
49M
| 1
|
SRR10298309
|
Li2021comprehensive
|
H. sapiens
|
GRO-seq
|
MDA-MB-231 (cell line)
| null | 1
|
59M
| 1
|
SRR10298310
|
Li2021comprehensive
|
H. sapiens
|
GRO-seq
|
MDA-MB-231 (cell line)
| null | 2
|
115M
| 2
|
SRR10312745
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
DMSO (6hr) , HCMV strain Towne IE2 BAC (4day)
| 1
|
28M
| 2
|
SRR10312746
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain Towne IE2 BAC (4day) , dTag7 (6hr)
| 1
|
29M
| 3
|
SRR10312747
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
DMSO (6hr) , HCMV strain Towne IE2F BAC (4day)
| 1
|
29M
| 2
|
SRR10312748
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain Towne IE2F BAC (4day) , dTag7 (6hr)
| 1
|
25M
| 3
|
SRR10312749
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
DMSO (6hr) , HCMV strain Towne IE2 BAC (4day) , flavopiridol (1hr)
| 1
|
27M
| 3
|
SRR10312750
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain Towne IE2 BAC (4day) , dTag7 (6hr) , flavopiridol (1hr)
| 1
|
28M
| 3
|
SRR10312751
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
DMSO (6hr) , HCMV strain Towne IE2F BAC (4day) , flavopiridol (1hr)
| 1
|
28M
| 3
|
SRR10312752
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain Towne IE2F BAC (4day) , dTag7 (6hr) , flavopiridol (1hr)
| 1
|
31M
| 3
|
SRR10312753
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
DMSO (6hr) , HCMV strain TB40/E IE2F (3day)
| 1
|
38M
| 4
|
SRR10312754
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain TB40/E IE2F (3day) , dTag7 (6hr)
| 1
|
43M
| 3
|
SRR10312755
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
DMSO (6hr) , HCMV strain TB40/E IE2F (3day) , flavopiridol (1hr)
| 1
|
40M
| 3
|
SRR10312756
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain TB40/E IE2F (3day) , dTag7 (6hr) , flavopiridol (1hr)
| 1
|
36M
| 4
|
SRR10312757
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
DMSO (6hr) , HCMV strain TB40/E IE2F (3day)
| 2
|
38M
| 4
|
SRR10312758
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain TB40/E IE2F (3day) , dTag7 (6hr)
| 2
|
26M
| 5
|
SRR10312759
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
DMSO (6hr) , HCMV strain TB40/E IE2F (3day) , phosphonoformic acid (6hr)
| 1
|
42M
| 3
|
SRR10312760
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain TB40/E IE2F (3day) , dTag7 (6hr) , phosphonoformic acid (6hr)
| 1
|
39M
| 4
|
SRR10312761
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain TB40/E IE2 (1day)
| 1
|
36M
| 3
|
SRR10312762
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain TB40/E IE2 (3day)
| 1
|
33M
| 3
|
SRR10312763
|
Li2020human
|
H. sapiens
|
PRO-seq
|
foreskin fibroblast (primary)
|
HCMV strain TB40/E IE2 (3day) , phosphonoformic acid (3day)
| 1
|
24M
| 4
|
SRR10354624
|
Jaeger2020selective
|
H. sapiens
|
PRO-seq
|
KBM7 (cell line)
|
DMSO (2hr)
| 1
|
77M
| 1
|
SRR10354625
|
Jaeger2020selective
|
H. sapiens
|
PRO-seq
|
KBM7 (cell line)
|
DMSO (2hr)
| 2
|
67M
| 1
|
SRR10354626
|
Jaeger2020selective
|
H. sapiens
|
PRO-seq
|
KBM7 (cell line)
|
dTAG7 (2hr)
| 1
|
74M
| 2
|
SRR10354627
|
Jaeger2020selective
|
H. sapiens
|
PRO-seq
|
KBM7 (cell line)
|
dTAG7 (2hr)
| 2
|
83M
| 1
|
SRR10354653
|
Jaeger2020selective
|
H. sapiens
|
other
|
KBM7 (cell line)
|
4-thiouridine (5min) , DMSO (2hr)
| 1
|
57M
| 1
|
SRR10354654
|
Jaeger2020selective
|
H. sapiens
|
other
|
KBM7 (cell line)
|
4-thiouridine (5min) , DMSO (2hr)
| 2
|
60M
| 1
|
SRR10354655
|
Jaeger2020selective
|
H. sapiens
|
other
|
KBM7 (cell line)
|
4-thiouridine (5min) , dTAG7 (2hr)
| 1
|
63M
| 1
|
SRR10354656
|
Jaeger2020selective
|
H. sapiens
|
other
|
KBM7 (cell line)
|
4-thiouridine (5min) , dTAG7 (2hr)
| 2
|
69M
| 1
|
SRR10354657
|
Jaeger2020selective
|
H. sapiens
|
other
|
KBM7 (cell line)
|
4-thiouridine (5min) , NVP2 (30min)
| 1
|
59M
| 2
|
SRR10354658
|
Jaeger2020selective
|
H. sapiens
|
other
|
KBM7 (cell line)
|
4-thiouridine (5min) , NVP2 (30min)
| 2
|
55M
| 1
|
SRR10354659
|
Jaeger2020selective
|
H. sapiens
|
other
|
KBM7 (cell line)
|
4-thiouridine (5min) , NVP2 (30min) , dTAG7 (2hr)
| 1
|
58M
| 1
|
End of preview.
Data pulled from https://nascent.colorado.edu/home/
Querying with DuckDB
duckdb -csv -c "SELECT * FROM read_csv_auto('~/src/fg/DBNascent/all_samples.csv') WHERE Protocol == 'GRO-seq' AND \"Cell type\" ILIKE '%HeLa%'"
# Write the output to a file
# > hela_groseq.csv
| Sample name | Paper identifier | Organism | Protocol | Cell type | Treatment | Replicate | Read depth | QC score |
|---|---|---|---|---|---|---|---|---|
| ERR769522 | Laitem2015cdk9 | H. sapiens | GRO-seq | HeLa (cell line) | DRB (30min) | 1 | 20M | 4 |
| ERR769523 | Laitem2015cdk9 | H. sapiens | GRO-seq | HeLa (cell line) | KM05283 (30min) | 1 | 23M | 4 |
| ERR769524 | Laitem2015cdk9 | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 24M | 2 |
| ERR769525 | Laitem2015cdk9 | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 2 | 26M | 2 |
| SRR1342250 | Gardini2014integrator | H. sapiens | GRO-seq | HeLa (cell line) | EGF (30min) , serum starvation (1day) | 1 | 58M | 3 |
| SRR1342251 | Gardini2014integrator | H. sapiens | GRO-seq | HeLa (cell line) | EGF (30min) , doxycycline (4day) , serum starvation (1day) | 1 | 45M | 1 |
| SRR1342252 | Gardini2014integrator | H. sapiens | GRO-seq | HeLa (cell line) | EGF (30min) , serum starvation (1day) | 2 | 114M | 4 |
| SRR1342253 | Gardini2014integrator | H. sapiens | GRO-seq | HeLa (cell line) | EGF (30min) , doxycycline (4day) , serum starvation (1day) | 2 | 71M | 3 |
| SRR1596500 | Andersson2014nuclear | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 21M | 1 |
| SRR1596501 | Andersson2014nuclear | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 2 | 33M | 1 |
| SRR2059423 | Zhang2016regulation | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 56M | 3 |
| SRR2059424 | Zhang2016regulation | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 85M | 3 |
| SRR5109939 | Bouvyliivrand2017analysis | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 22M | 1 |
| SRR7010982 | Fei2018ndf | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 64M | 2 |
| SRR7010983 | Fei2018ndf | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 76M | 2 |
| SRR7010984 | Fei2018ndf | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 2 | 66M | 2 |
| SRZ10004434 | Bahat2019targeting | H. sapiens | GRO-seq | HeLa (cell line) | DMSO (90min) | 1 | 141M | 2 |
| SRZ10004438 | Bahat2019targeting | H. sapiens | GRO-seq | HeLa (cell line) | DMSO (90min) | 2 | 124M | 2 |
| SRZ10004442 | Bahat2019targeting | H. sapiens | GRO-seq | HeLa (cell line) | Spt5-Pol II small-molecule inhibitor 21 (90min) | 1 | 138M | 2 |
| SRZ1693611 | Duttke2015human | H. sapiens | GRO-seq | HeLa (cell line) | NaN | 1 | 68M | 4 |
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