{
"@context": "/terms/",
"@id": "/alignment-files/IGVFFI2631HESV/",
"@type": [
"AlignmentFile",
"File",
"Item"
],
"accession": "IGVFFI2631HESV",
"aliases": [
"charles-gersbach:alignment-set-bulk-atac-control-ipsc-cm-rep1"
],
"analysis_step_version": "/analysis-step-versions/c95d766a-a900-4694-8065-e12651f618ba/",
"assay_titles": [
"ATAC-seq"
],
"assembly": "GRCh38",
"audit": {},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"content_md5sum": "b2f3110ee2893fe47c68832f353c86f5",
"content_summary": "filtered alignments",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-28T18:06:59.747225+00:00",
"derived_from": [
"/sequence-files/IGVFFI9646HDEO/",
"/sequence-files/IGVFFI5115MUFD/"
],
"file_format": "bam",
"file_set": {
"@id": "/analysis-sets/IGVFDS4606DSTJ/",
"accession": "IGVFDS4606DSTJ",
"file_set_type": "intermediate analysis",
"samples": [
{
"@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/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/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/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/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/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: alignments"
},
"file_size": 1935905372,
"filtered": true,
"gene_list_for": [],
"href": "/alignment-files/IGVFFI2631HESV/@@download/IGVFFI2631HESV.bam",
"input_file_for": [
"/tabular-files/IGVFFI9763CJKG/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"loci_list_for": [],
"md5sum": "18cfa9a697f14a3bf79a9a7abaf78114",
"read_count": 54269143,
"redacted": false,
"reference_files": [
"/reference-files/IGVFFI6815WBWB/"
],
"release_timestamp": "2024-12-03T20:43:50.865061+00:00",
"s3_uri": "s3://igvf-files/2024/10/28/4aab682a-91c9-4555-8e19-f7e514aea185/IGVFFI2631HESV.bam",
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFdatasubmission/TaylorHiCAR/ATAC/Control_1.masked.dups_marked.bam",
"summary": "GRCh38 filtered alignments",
"upload_status": "validated",
"uuid": "4aab682a-91c9-4555-8e19-f7e514aea185"
}