{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8192PAOP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8192PAOP",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf6_10x3"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7537OHFN/",
"accession": "IGVFDS7537OHFN",
"aliases": [
"ansuman-satpathy:multiseq_igvf6_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": [],
"creation_timestamp": "2024-07-22T00:31:55.480787+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO6638HIAD/",
"accession": "IGVFDO6638HIAD",
"aliases": [
"igvf:donor_of_H1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5485ZKZD/",
"accession": "IGVFFI5485ZKZD",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS1_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:58:16.732590+00:00",
"file_format": "fastq",
"file_size": 9590461807,
"href": "/sequence-files/IGVFFI5485ZKZD/@@download/IGVFFI5485ZKZD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/aab81889-d83d-4f29-b65f-9235c1df56a8/IGVFFI5485ZKZD.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L005_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6599XMXP/",
"accession": "IGVFFI6599XMXP",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS3_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:04:55.452007+00:00",
"file_format": "fastq",
"file_size": 2111553218,
"href": "/sequence-files/IGVFFI6599XMXP/@@download/IGVFFI6599XMXP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/2e68b61b-c182-4dd8-b863-2d081c611e47/IGVFFI6599XMXP.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L007_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9344ZUUY/",
"accession": "IGVFFI9344ZUUY",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS2_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:01:56.458026+00:00",
"file_format": "fastq",
"file_size": 2113118503,
"href": "/sequence-files/IGVFFI9344ZUUY/@@download/IGVFFI9344ZUUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/ccfd051e-e37d-470e-a968-a38e602ee121/IGVFFI9344ZUUY.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2850PJAV/",
"accession": "IGVFFI2850PJAV",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS3_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:04:07.516204+00:00",
"file_format": "fastq",
"file_size": 9746459798,
"href": "/sequence-files/IGVFFI2850PJAV/@@download/IGVFFI2850PJAV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/ef06fbc2-9315-4aac-b0cf-e851368a0a7c/IGVFFI2850PJAV.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L007_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2773UHYP/",
"accession": "IGVFFI2773UHYP",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS2_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:59:31.990656+00:00",
"file_format": "fastq",
"file_size": 9622512322,
"href": "/sequence-files/IGVFFI2773UHYP/@@download/IGVFFI2773UHYP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/5c087747-158b-47d6-b8d8-929a6bccdca2/IGVFFI2773UHYP.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2601DFWA/",
"accession": "IGVFFI2601DFWA",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:56:43.756712+00:00",
"file_format": "fastq",
"file_size": 9559909905,
"href": "/sequence-files/IGVFFI2601DFWA/@@download/IGVFFI2601DFWA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/cc04a817-1cb6-4ef4-a04f-a423949441de/IGVFFI2601DFWA.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4733OFMI/",
"accession": "IGVFFI4733OFMI",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:57:32.216272+00:00",
"file_format": "fastq",
"file_size": 5189052562,
"href": "/sequence-files/IGVFFI4733OFMI/@@download/IGVFFI4733OFMI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/7c8a225a-370d-4cb2-bc71-4c400a4e7d5a/IGVFFI4733OFMI.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8903FVZQ/",
"accession": "IGVFFI8903FVZQ",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:59:01.207755+00:00",
"file_format": "fastq",
"file_size": 2105675239,
"href": "/sequence-files/IGVFFI8903FVZQ/@@download/IGVFFI8903FVZQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/80f76375-2cb2-43c7-b160-f21771582367/IGVFFI8903FVZQ.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3900KETJ/",
"accession": "IGVFFI3900KETJ",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS2_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:00:24.671764+00:00",
"file_format": "fastq",
"file_size": 5221737002,
"href": "/sequence-files/IGVFFI3900KETJ/@@download/IGVFFI3900KETJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/48315b6f-28c0-4e76-a025-7bc9ba1712e8/IGVFFI3900KETJ.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3700SAVO/",
"accession": "IGVFFI3700SAVO",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS2_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:01:06.710263+00:00",
"file_format": "fastq",
"file_size": 9640866131,
"href": "/sequence-files/IGVFFI3700SAVO/@@download/IGVFFI3700SAVO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/a1f86f07-cd1a-4950-af14-81e27a2ffbc5/IGVFFI3700SAVO.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L006_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4734VGRO/",
"accession": "IGVFFI4734VGRO",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS3_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:02:26.803327+00:00",
"file_format": "fastq",
"file_size": 9698089258,
"href": "/sequence-files/IGVFFI4734VGRO/@@download/IGVFFI4734VGRO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/30bec3c1-1c66-452b-aa73-f5514170f62e/IGVFFI4734VGRO.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2779ZFRT/",
"accession": "IGVFFI2779ZFRT",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x3_NGS3_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:03:22.025324+00:00",
"file_format": "fastq",
"file_size": 5277712596,
"href": "/sequence-files/IGVFFI2779ZFRT/@@download/IGVFFI2779ZFRT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/a9bc1dca-edc2-429c-8f65-1c5f03694b5b/IGVFFI2779ZFRT.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/230522_IGVF6_McGinnis/ATAC/FASTQ/ATAC_3_S7_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0212NGQJ/",
"accession": "IGVFFI0212NGQJ",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp6_atac_10x3_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:41:53.811119+00:00",
"file_format": "yaml",
"file_size": 1374,
"href": "/configuration-files/IGVFFI0212NGQJ/@@download/IGVFFI0212NGQJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/841cd32d-4357-4be9-8ffb-1f112202c10f/IGVFFI0212NGQJ.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp6_atac_10x3_NGS1_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5424XQWP/",
"accession": "IGVFFI5424XQWP",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp6_atac_10x3_NGS3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:42:00.826776+00:00",
"file_format": "yaml",
"file_size": 1375,
"href": "/configuration-files/IGVFFI5424XQWP/@@download/IGVFFI5424XQWP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/4ef42e62-1fff-4964-81d7-85cd515f3509/IGVFFI5424XQWP.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp6_atac_10x3_NGS3_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9131WYLW/",
"accession": "IGVFFI9131WYLW",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp6_atac_10x3_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:41:57.103228+00:00",
"file_format": "yaml",
"file_size": 1375,
"href": "/configuration-files/IGVFFI9131WYLW/@@download/IGVFFI9131WYLW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/3acf89bd-2b33-4db8-b57b-9137b9817ac3/IGVFFI9131WYLW.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp6_atac_10x3_NGS2_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3232NVVG/"
],
"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/IGVFDS4668AHMA/",
"accession": "IGVFDS4668AHMA",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:12:48.388987+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8276PHGD/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8276PHGD",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf6_10x3"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003042/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H1"
],
"status": "released",
"summary": "H1-hESC",
"term_name": "H1-hESC"
}
],
"status": "released",
"summary": "multiplexed sample: H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days, male, Homo sapiens; H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 days, male, Homo sapiens; ... and 6 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-22T17:04:08.099782+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
"uuid": "28d8bafe-2cdf-4f68-9d6a-5d4df71ddc6a"
}