{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8054AFXK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8054AFXK",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf12_10x3"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM7114MTSH](/multiplexed-samples/IGVFSM7114MTSH/) has in progress subobject tabular file [IGVFFI6870GMPP](/tabular-files/IGVFFI6870GMPP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM7114MTSH/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM7114MTSH](/multiplexed-samples/IGVFSM7114MTSH/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/multiplexed-samples/IGVFSM7114MTSH/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS8701GVWQ](/auxiliary-sets/IGVFDS8701GVWQ/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/auxiliary-sets/IGVFDS8701GVWQ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8054AFXK](/measurement-sets/IGVFDS8054AFXK/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS8054AFXK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8054AFXK](/measurement-sets/IGVFDS8054AFXK/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS8054AFXK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8701GVWQ/",
"accession": "IGVFDS8701GVWQ",
"aliases": [
"ansuman-satpathy:multiseq_igvf12_10x3"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
}
],
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"controlled_access": true,
"creation_timestamp": "2024-07-23T20:58:54.038595+00:00",
"data_use_limitation_summaries": [
"GRU"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1264SGCS/",
"accession": "IGVFDO1264SGCS",
"aliases": [
"ansuman-satpathy:bridge_bone_marrow_donor_2038"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1718HCES/",
"accession": "IGVFDO1718HCES",
"aliases": [
"ansuman-satpathy:singh_bcell_donor_1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"aliases": [
"ansuman-satpathy:singh_bcell_donor_2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8558PNDV/",
"accession": "IGVFFI8558PNDV",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS1_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:12:19.563845+00:00",
"file_format": "fastq",
"file_size": 1191797498,
"href": "/sequence-files/IGVFFI8558PNDV/@@download/IGVFFI8558PNDV.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/a686f61d-d485-4e1c-a692-213e7c587fde/IGVFFI8558PNDV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S22_L007_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4060UQYO/",
"accession": "IGVFFI4060UQYO",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS3_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:23:30.790594+00:00",
"file_format": "fastq",
"file_size": 1191602493,
"href": "/sequence-files/IGVFFI4060UQYO/@@download/IGVFFI4060UQYO.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/98eb9481-cd33-4e23-8ac2-96fd1e18f0fb/IGVFFI4060UQYO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5681MMWZ/",
"accession": "IGVFFI5681MMWZ",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS1_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:16:39.137497+00:00",
"file_format": "fastq",
"file_size": 5171376677,
"href": "/sequence-files/IGVFFI5681MMWZ/@@download/IGVFFI5681MMWZ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/35b30761-5633-4411-a1bd-b8cf88ab6c52/IGVFFI5681MMWZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S22_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1601EYWS/",
"accession": "IGVFFI1601EYWS",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS1_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:17:38.539538+00:00",
"file_format": "fastq",
"file_size": 2790985361,
"href": "/sequence-files/IGVFFI1601EYWS/@@download/IGVFFI1601EYWS.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/ee7369a3-0cda-485c-ae0c-42385a1b5e56/IGVFFI1601EYWS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S22_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9559PSYF/",
"accession": "IGVFFI9559PSYF",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS2_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:21:23.588822+00:00",
"file_format": "fastq",
"file_size": 2803526844,
"href": "/sequence-files/IGVFFI9559PSYF/@@download/IGVFFI9559PSYF.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/09393a66-8665-4c2f-92c5-e07cc187adef/IGVFFI9559PSYF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S22_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2760CRWI/",
"accession": "IGVFFI2760CRWI",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS2_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:19:39.874824+00:00",
"file_format": "fastq",
"file_size": 1189634234,
"href": "/sequence-files/IGVFFI2760CRWI/@@download/IGVFFI2760CRWI.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/a5089c89-6264-4ebd-a31c-435c8732b27a/IGVFFI2760CRWI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S22_L008_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1053YOSQ/",
"accession": "IGVFFI1053YOSQ",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS1_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:18:32.896230+00:00",
"file_format": "fastq",
"file_size": 5084762759,
"href": "/sequence-files/IGVFFI1053YOSQ/@@download/IGVFFI1053YOSQ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/37fd529a-8048-47ea-b130-a7ee0afe476b/IGVFFI1053YOSQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S22_L007_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6662PVEM/",
"accession": "IGVFFI6662PVEM",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS5_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:32:12.967593+00:00",
"file_format": "fastq",
"file_size": 1180793246,
"href": "/sequence-files/IGVFFI6662PVEM/@@download/IGVFFI6662PVEM.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/778031e3-7d74-491e-8401-364903811041/IGVFFI6662PVEM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5240ZVKF/",
"accession": "IGVFFI5240ZVKF",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS2_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:20:18.137707+00:00",
"file_format": "fastq",
"file_size": 5172481058,
"href": "/sequence-files/IGVFFI5240ZVKF/@@download/IGVFFI5240ZVKF.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/6f8c79c9-3d5e-448a-980b-9e81cc876602/IGVFFI5240ZVKF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S22_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2711CHJQ/",
"accession": "IGVFFI2711CHJQ",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS4_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:28:00.975686+00:00",
"file_format": "fastq",
"file_size": 1190958075,
"href": "/sequence-files/IGVFFI2711CHJQ/@@download/IGVFFI2711CHJQ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/45340efe-b2f3-4223-8435-f80c47453bda/IGVFFI2711CHJQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1803NYGI/",
"accession": "IGVFFI1803NYGI",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS2_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:22:25.889041+00:00",
"file_format": "fastq",
"file_size": 5105412498,
"href": "/sequence-files/IGVFFI1803NYGI/@@download/IGVFFI1803NYGI.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/098f7de2-541e-44e2-89e2-91a52ab9e727/IGVFFI1803NYGI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S22_L008_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4139NKOX/",
"accession": "IGVFFI4139NKOX",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS7_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:43:48.197318+00:00",
"file_format": "fastq",
"file_size": 5067282786,
"href": "/sequence-files/IGVFFI4139NKOX/@@download/IGVFFI4139NKOX.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/8d93e5b7-a38b-44bb-bac0-804f12aaba9a/IGVFFI4139NKOX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L007_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9868ZRIJ/",
"accession": "IGVFFI9868ZRIJ",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS4_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:30:53.344339+00:00",
"file_format": "fastq",
"file_size": 4989036796,
"href": "/sequence-files/IGVFFI9868ZRIJ/@@download/IGVFFI9868ZRIJ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/cf46bed1-a77d-41d8-91e8-6a80e10baff3/IGVFFI9868ZRIJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4901YPGO/",
"accession": "IGVFFI4901YPGO",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS3_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:24:28.536126+00:00",
"file_format": "fastq",
"file_size": 5029983623,
"href": "/sequence-files/IGVFFI4901YPGO/@@download/IGVFFI4901YPGO.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/3c750e59-df5d-47e0-99b2-dda7743e94dc/IGVFFI4901YPGO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2860TARJ/",
"accession": "IGVFFI2860TARJ",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS3_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:25:38.997568+00:00",
"file_format": "fastq",
"file_size": 2744274904,
"href": "/sequence-files/IGVFFI2860TARJ/@@download/IGVFFI2860TARJ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/0f1b4aa0-0ee6-48bf-a533-d30f5bd23df5/IGVFFI2860TARJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3942DQSL/",
"accession": "IGVFFI3942DQSL",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS3_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:26:44.342417+00:00",
"file_format": "fastq",
"file_size": 4970055483,
"href": "/sequence-files/IGVFFI3942DQSL/@@download/IGVFFI3942DQSL.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/dafc85da-b573-4cea-9a2a-5f8332d718ed/IGVFFI3942DQSL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L003_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3001RHDA/",
"accession": "IGVFFI3001RHDA",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS5_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:33:04.343281+00:00",
"file_format": "fastq",
"file_size": 5021035778,
"href": "/sequence-files/IGVFFI3001RHDA/@@download/IGVFFI3001RHDA.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/5a05c1c2-333a-439a-9b59-fb3a4267683e/IGVFFI3001RHDA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8344JOAY/",
"accession": "IGVFFI8344JOAY",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS4_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:28:54.419474+00:00",
"file_format": "fastq",
"file_size": 5049039620,
"href": "/sequence-files/IGVFFI8344JOAY/@@download/IGVFFI8344JOAY.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/40578e4a-50df-46ab-bad7-528a88970dc7/IGVFFI8344JOAY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4301VLFP/",
"accession": "IGVFFI4301VLFP",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS4_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:30:01.615726+00:00",
"file_format": "fastq",
"file_size": 2750271708,
"href": "/sequence-files/IGVFFI4301VLFP/@@download/IGVFFI4301VLFP.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/60e7b167-c75e-4177-bc45-b93b5df0c6dd/IGVFFI4301VLFP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5828JUEI/",
"accession": "IGVFFI5828JUEI",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS5_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:34:18.914707+00:00",
"file_format": "fastq",
"file_size": 2729874479,
"href": "/sequence-files/IGVFFI5828JUEI/@@download/IGVFFI5828JUEI.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/ab924cd8-35f0-48d9-bc88-b8eba0a600b2/IGVFFI5828JUEI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1035VYAY/",
"accession": "IGVFFI1035VYAY",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS5_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:35:09.311539+00:00",
"file_format": "fastq",
"file_size": 4953858642,
"href": "/sequence-files/IGVFFI1035VYAY/@@download/IGVFFI1035VYAY.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/634b14f2-6f20-4444-a82a-886a55d1d3f0/IGVFFI1035VYAY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L005_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1860HCWQ/",
"accession": "IGVFFI1860HCWQ",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS6_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:36:42.228075+00:00",
"file_format": "fastq",
"file_size": 1178276106,
"href": "/sequence-files/IGVFFI1860HCWQ/@@download/IGVFFI1860HCWQ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/3a23d9af-b7ca-4563-bc3f-b3bb68bdf838/IGVFFI1860HCWQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1683SSJR/",
"accession": "IGVFFI1683SSJR",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS6_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:37:29.043800+00:00",
"file_format": "fastq",
"file_size": 5014673447,
"href": "/sequence-files/IGVFFI1683SSJR/@@download/IGVFFI1683SSJR.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/f1d0231e-ea89-421d-a3e5-2556bbb4a4ea/IGVFFI1683SSJR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6867YZGN/",
"accession": "IGVFFI6867YZGN",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS6_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:38:43.036110+00:00",
"file_format": "fastq",
"file_size": 2723262487,
"href": "/sequence-files/IGVFFI6867YZGN/@@download/IGVFFI6867YZGN.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/34a92101-5002-4df8-8600-a4c99ab0c090/IGVFFI6867YZGN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8693EMGC/",
"accession": "IGVFFI8693EMGC",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS6_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:39:26.048966+00:00",
"file_format": "fastq",
"file_size": 4938566728,
"href": "/sequence-files/IGVFFI8693EMGC/@@download/IGVFFI8693EMGC.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/071ee5d1-ae0a-48ed-9e34-3d2951610e5e/IGVFFI8693EMGC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L006_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4842PFEE/",
"accession": "IGVFFI4842PFEE",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS7_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:40:55.139901+00:00",
"file_format": "fastq",
"file_size": 1198209493,
"href": "/sequence-files/IGVFFI4842PFEE/@@download/IGVFFI4842PFEE.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/3aa2ff68-8495-459e-911b-747d5c927fae/IGVFFI4842PFEE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L007_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3768JKDM/",
"accession": "IGVFFI3768JKDM",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS7_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:41:41.844536+00:00",
"file_format": "fastq",
"file_size": 5146179418,
"href": "/sequence-files/IGVFFI3768JKDM/@@download/IGVFFI3768JKDM.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/56c7c5b1-ec0b-42e1-a199-5319419b496d/IGVFFI3768JKDM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0919ZFSC/",
"accession": "IGVFFI0919ZFSC",
"aliases": [
"ansuman-satpathy:igvf_exp12_atac_10x3_NGS7_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T22:42:57.182908+00:00",
"file_format": "fastq",
"file_size": 2800186826,
"href": "/sequence-files/IGVFFI0919ZFSC/@@download/IGVFFI0919ZFSC.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/2e3b7b26-e121-433f-ae3a-5045317e4bea/IGVFFI0919ZFSC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/240425_IGVF12_McGinnis/ATAC/FASTQ/ATAC3_S7_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0578WYCU/",
"accession": "IGVFFI0578WYCU",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp12_atac_10x3_NGS4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:25:15.327080+00:00",
"file_format": "yaml",
"file_size": 1379,
"href": "/configuration-files/IGVFFI0578WYCU/@@download/IGVFFI0578WYCU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/2c520f01-4ff1-4814-bc3b-97abf1ea6f0f/IGVFFI0578WYCU.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp12_atac_10x3_NGS4_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8809TWFX/",
"accession": "IGVFFI8809TWFX",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp12_atac_10x3_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:25:08.561783+00:00",
"file_format": "yaml",
"file_size": 1372,
"href": "/configuration-files/IGVFFI8809TWFX/@@download/IGVFFI8809TWFX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/9af128f1-47d0-4ff4-a769-306d924d75e5/IGVFFI8809TWFX.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp12_atac_10x3_NGS2_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5684KGUN/",
"accession": "IGVFFI5684KGUN",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp12_atac_10x3_NGS7"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:25:26.662255+00:00",
"file_format": "yaml",
"file_size": 1377,
"href": "/configuration-files/IGVFFI5684KGUN/@@download/IGVFFI5684KGUN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/b27f4670-1507-4d0d-a0a9-5f237ae5f7c5/IGVFFI5684KGUN.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp12_atac_10x3_NGS7_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6692RJTC/",
"accession": "IGVFFI6692RJTC",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp12_atac_10x3_NGS5"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:25:18.853754+00:00",
"file_format": "yaml",
"file_size": 1378,
"href": "/configuration-files/IGVFFI6692RJTC/@@download/IGVFFI6692RJTC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/eaaddc48-a026-46a9-ae2d-2e60f13a8389/IGVFFI6692RJTC.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp12_atac_10x3_NGS5_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5578KKXO/",
"accession": "IGVFFI5578KKXO",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp12_atac_10x3_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:25:05.162737+00:00",
"file_format": "yaml",
"file_size": 1379,
"href": "/configuration-files/IGVFFI5578KKXO/@@download/IGVFFI5578KKXO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/043509d6-4718-4f61-b3a0-646d00e40559/IGVFFI5578KKXO.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp12_atac_10x3_NGS1_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6682VSMM/",
"accession": "IGVFFI6682VSMM",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp12_atac_10x3_NGS3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:25:11.870342+00:00",
"file_format": "yaml",
"file_size": 1374,
"href": "/configuration-files/IGVFFI6682VSMM/@@download/IGVFFI6682VSMM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/0755c0a5-9498-4809-83cc-620a1e89db60/IGVFFI6682VSMM.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp12_atac_10x3_NGS3_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2943PZNZ/",
"accession": "IGVFFI2943PZNZ",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp12_atac_10x3_NGS6"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:25:22.832369+00:00",
"file_format": "yaml",
"file_size": 1379,
"href": "/configuration-files/IGVFFI2943PZNZ/@@download/IGVFFI2943PZNZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/a4650829-be03-4773-9965-721549f47652/IGVFFI2943PZNZ.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp12_atac_10x3_NGS6_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3005LSBM/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI7587TJLC/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome with MULTI-seq",
"protocols": [
"https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS5862OZVJ/",
"accession": "IGVFDS5862OZVJ",
"status": "released"
}
],
"release_timestamp": "2025-03-22T00:38:48.720056+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7114MTSH/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7114MTSH",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf12_10x3"
],
"classifications": [
"differentiated cell specimen",
"tissue",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/1e03eda3-a983-4cee-864e-43acb4c1b186/",
"certificate_identifier": "IP115-18",
"controlled_access": true,
"data_use_limitation": "GRU",
"status": "released"
},
{
"@id": "/institutional-certificates/460c2060-3b32-43c1-ab4b-b2ef0fbeb2b2/",
"certificate_identifier": "IP115-22",
"controlled_access": true,
"data_use_limitation": "GRU",
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "B cell",
"term_name": "B cell"
},
{
"@id": "/sample-terms/UBERON_0002371/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "bone marrow",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days; Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-23T22:12:19.563845+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
"uuid": "997fc43a-4908-4a1f-9c71-55e54e161883"
}