{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI9763CJKG/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI9763CJKG",
"aliases": [
"charles-gersbach:tabular-file-bulk-atac-count"
],
"analysis_step_version": "/analysis-step-versions/6eedb442-9e3c-4b7f-b666-6b983f47aa15/",
"assay_titles": [
"ATAC-seq"
],
"assembly": "GRCh38",
"audit": {},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"barcode_map_for": [],
"content_md5sum": "f8c8be6cb7545280ffef99f40e9d4376",
"content_type": "peak quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-28T17:07:10.116373+00:00",
"derived_from": [
"/alignment-files/IGVFFI1534IVYM/",
"/alignment-files/IGVFFI2179LWNB/",
"/alignment-files/IGVFFI4382XXOK/",
"/alignment-files/IGVFFI2631HESV/",
"/alignment-files/IGVFFI3796FCTL/",
"/alignment-files/IGVFFI4523VJXB/"
],
"file_format": "tsv",
"file_format_specifications": [
"/documents/d604ae54-e814-4a59-8523-eb2deb7f7841/"
],
"file_set": {
"@id": "/analysis-sets/IGVFDS9490WNXZ/",
"accession": "IGVFDS9490WNXZ",
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7187NNQU/",
"accession": "IGVFSM7187NNQU",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM4983MYZQ/",
"accession": "IGVFSM4983MYZQ",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM6698FQIG/",
"accession": "IGVFSM6698FQIG",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens treated with 4 μM GSK3 inhibition for 7 days",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/98ba0c5c-8005-41bc-bcbb-6c6eff41af4e/",
"purpose": "antagonist",
"status": "released",
"summary": "Treatment of 4 μM GSK3 inhibition for 7 days",
"treatment_term_name": "GSK3 inhibition"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM5361EAGX/",
"accession": "IGVFSM5361EAGX",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens treated with 4 μM GSK3 inhibition for 7 days",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/98ba0c5c-8005-41bc-bcbb-6c6eff41af4e/",
"purpose": "antagonist",
"status": "released",
"summary": "Treatment of 4 μM GSK3 inhibition for 7 days",
"treatment_term_name": "GSK3 inhibition"
}
]
},
{
"@id": "/in-vitro-systems/IGVFSM9739CNEQ/",
"accession": "IGVFSM9739CNEQ",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9172PRNN/",
"accession": "IGVFSM9172PRNN",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens treated with 4 μM GSK3 inhibition for 7 days",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/98ba0c5c-8005-41bc-bcbb-6c6eff41af4e/",
"purpose": "antagonist",
"status": "released",
"summary": "Treatment of 4 μM GSK3 inhibition for 7 days",
"treatment_term_name": "GSK3 inhibition"
}
]
}
],
"status": "released",
"summary": "ATAC-seq: fold change over control, peak quantifications"
},
"file_size": 4343150,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI9763CJKG/@@download/IGVFFI9763CJKG.tsv.gz",
"input_file_for": [
"/tabular-files/IGVFFI7417ASXN/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"loci_list_for": [],
"md5sum": "91559b17fd4b62d16d58f46b3a20b101",
"release_timestamp": "2024-12-03T20:43:50.351672+00:00",
"s3_uri": "s3://igvf-files/2024/10/28/108a447b-66f7-44c4-90ce-9b7c94ec39a5/IGVFFI9763CJKG.tsv.gz",
"schema_version": "13",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/ATAC/atacseq_counts.tsv.gz",
"summary": "GRCh38 peak quantifications",
"upload_status": "validated",
"uuid": "108a447b-66f7-44c4-90ce-9b7c94ec39a5"
}