{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1381KOVA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1381KOVA",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf17_10x4"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"audit": {},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5763YUNI/",
"accession": "IGVFDS5763YUNI",
"aliases": [
"ansuman-satpathy:multiseq_igvf17_10x4"
],
"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": "2025-01-27T22:55:45.526993+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO5261UCLF/",
"accession": "IGVFDO5261UCLF",
"aliases": [
"igvf:donor_of_RUES2",
"igvf:donor_RUES2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7133BHFZ/",
"accession": "IGVFFI7133BHFZ",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:29:43.022720+00:00",
"file_format": "fastq",
"file_size": 4329514772,
"href": "/sequence-files/IGVFFI7133BHFZ/@@download/IGVFFI7133BHFZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/119faec6-69eb-426b-a79f-a828707d0827/IGVFFI7133BHFZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7598TGFL/",
"accession": "IGVFFI7598TGFL",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS2_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:32:39.065111+00:00",
"file_format": "fastq",
"file_size": 8409196724,
"href": "/sequence-files/IGVFFI7598TGFL/@@download/IGVFFI7598TGFL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/74142b37-e5e8-45b5-98dc-a2a2d589824c/IGVFFI7598TGFL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1115MCGP/",
"accession": "IGVFFI1115MCGP",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS3_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:33:27.074574+00:00",
"file_format": "fastq",
"file_size": 1224358149,
"href": "/sequence-files/IGVFFI1115MCGP/@@download/IGVFFI1115MCGP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/f3ea20c9-b3b4-4990-9681-beb533641ada/IGVFFI1115MCGP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L007_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0978CLLR/",
"accession": "IGVFFI0978CLLR",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS3_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:34:38.555855+00:00",
"file_format": "fastq",
"file_size": 8484751412,
"href": "/sequence-files/IGVFFI0978CLLR/@@download/IGVFFI0978CLLR.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/278d6699-af1c-477c-9ffc-b1710669ddc7/IGVFFI0978CLLR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1240VNKQ/",
"accession": "IGVFFI1240VNKQ",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS2_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:31:37.657089+00:00",
"file_format": "fastq",
"file_size": 1216487122,
"href": "/sequence-files/IGVFFI1240VNKQ/@@download/IGVFFI1240VNKQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/4cddfe3b-19ca-493c-8cbe-e2f5a99f0539/IGVFFI1240VNKQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8735GPEL/",
"accession": "IGVFFI8735GPEL",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS3_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:33:39.595172+00:00",
"file_format": "fastq",
"file_size": 1231662778,
"href": "/sequence-files/IGVFFI8735GPEL/@@download/IGVFFI8735GPEL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/207f1c48-8e81-4a5f-ac45-a32b2b0b08a0/IGVFFI8735GPEL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L007_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7108OWMP/",
"accession": "IGVFFI7108OWMP",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS2_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:31:22.061594+00:00",
"file_format": "fastq",
"file_size": 1211736495,
"href": "/sequence-files/IGVFFI7108OWMP/@@download/IGVFFI7108OWMP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/b3549339-7f1f-432f-b00f-ceada1e926ee/IGVFFI7108OWMP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7934ZMBN/",
"accession": "IGVFFI7934ZMBN",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS4_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:36:32.232006+00:00",
"file_format": "fastq",
"file_size": 8476900017,
"href": "/sequence-files/IGVFFI7934ZMBN/@@download/IGVFFI7934ZMBN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/bcfface5-9da2-4e1b-ab47-52fe82808d89/IGVFFI7934ZMBN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4582RUSA/",
"accession": "IGVFFI4582RUSA",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:29:06.116326+00:00",
"file_format": "fastq",
"file_size": 1209319084,
"href": "/sequence-files/IGVFFI4582RUSA/@@download/IGVFFI4582RUSA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/04ed413e-b91b-4fa3-b7e5-e5a10202d5f3/IGVFFI4582RUSA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1076NVIH/",
"accession": "IGVFFI1076NVIH",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS1_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:29:19.597419+00:00",
"file_format": "fastq",
"file_size": 1229260830,
"href": "/sequence-files/IGVFFI1076NVIH/@@download/IGVFFI1076NVIH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/f226ddd3-069e-483c-9f6e-29c58b6a4dcd/IGVFFI1076NVIH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2690MYQF/",
"accession": "IGVFFI2690MYQF",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:30:26.829476+00:00",
"file_format": "fastq",
"file_size": 8434599179,
"href": "/sequence-files/IGVFFI2690MYQF/@@download/IGVFFI2690MYQF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/683875f4-5d03-4b90-8cb1-2cc01ca839cd/IGVFFI2690MYQF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6271BZLD/",
"accession": "IGVFFI6271BZLD",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS2_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:31:59.756400+00:00",
"file_format": "fastq",
"file_size": 4315745822,
"href": "/sequence-files/IGVFFI6271BZLD/@@download/IGVFFI6271BZLD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/508e1fb5-16a1-45f6-bb20-9ee4dba91884/IGVFFI6271BZLD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0262MIVJ/",
"accession": "IGVFFI0262MIVJ",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS3_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:33:58.850689+00:00",
"file_format": "fastq",
"file_size": 4346249980,
"href": "/sequence-files/IGVFFI0262MIVJ/@@download/IGVFFI0262MIVJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/ec707288-2073-40aa-9eac-3273b3e963c9/IGVFFI0262MIVJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7374OCNF/",
"accession": "IGVFFI7374OCNF",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS4_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:35:21.104456+00:00",
"file_format": "fastq",
"file_size": 1255112954,
"href": "/sequence-files/IGVFFI7374OCNF/@@download/IGVFFI7374OCNF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/2984a4be-30dc-425c-90bb-f72971d0974b/IGVFFI7374OCNF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L008_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7951TRNJ/",
"accession": "IGVFFI7951TRNJ",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS4_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:35:34.951137+00:00",
"file_format": "fastq",
"file_size": 1234356090,
"href": "/sequence-files/IGVFFI7951TRNJ/@@download/IGVFFI7951TRNJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/11321b25-7994-43fa-ac5b-ece05da52e12/IGVFFI7951TRNJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L008_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9066SKTV/",
"accession": "IGVFFI9066SKTV",
"aliases": [
"ansuman-satpathy:igvf_exp17_rna_10x4_NGS4_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:35:53.418981+00:00",
"file_format": "fastq",
"file_size": 4390667959,
"href": "/sequence-files/IGVFFI9066SKTV/@@download/IGVFFI9066SKTV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/a46cc568-4df4-4790-ae2d-73b2db3237f3/IGVFFI9066SKTV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/igvf17/GEX/CMAS19_GEX4_S168_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1249ATUC/",
"accession": "IGVFFI1249ATUC",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp17_rna_10x4_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2025-02-26T01:40:04.969183+00:00",
"file_format": "yaml",
"file_size": 1395,
"href": "/configuration-files/IGVFFI1249ATUC/@@download/IGVFFI1249ATUC.yaml.gz",
"s3_uri": "s3://igvf-files/2025/02/26/be3b6301-c6aa-4a11-b6c5-08f737de6d3e/IGVFFI1249ATUC.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_exp17_rna_10x4_NGS1_rna_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4299ENXR/",
"accession": "IGVFFI4299ENXR",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp17_rna_10x4_NGS4"
],
"content_type": "seqspec",
"creation_timestamp": "2025-02-26T01:40:18.920747+00:00",
"file_format": "yaml",
"file_size": 1396,
"href": "/configuration-files/IGVFFI4299ENXR/@@download/IGVFFI4299ENXR.yaml.gz",
"s3_uri": "s3://igvf-files/2025/02/26/e4a234e9-b3e8-4eb5-9bba-cd3a9826ed63/IGVFFI4299ENXR.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_exp17_rna_10x4_NGS4_rna_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2092KOLG/",
"accession": "IGVFFI2092KOLG",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp17_rna_10x4_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2025-02-26T01:40:09.268935+00:00",
"file_format": "yaml",
"file_size": 1394,
"href": "/configuration-files/IGVFFI2092KOLG/@@download/IGVFFI2092KOLG.yaml.gz",
"s3_uri": "s3://igvf-files/2025/02/26/9f940794-e4ce-410e-9cb3-a855de108cc4/IGVFFI2092KOLG.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_exp17_rna_10x4_NGS2_rna_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9573OXCH/",
"accession": "IGVFFI9573OXCH",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp17_rna_10x4_NGS3"
],
"content_type": "seqspec",
"creation_timestamp": "2025-02-26T01:40:13.749200+00:00",
"file_format": "yaml",
"file_size": 1395,
"href": "/configuration-files/IGVFFI9573OXCH/@@download/IGVFFI9573OXCH.yaml.gz",
"s3_uri": "s3://igvf-files/2025/02/26/afd72d2d-79f4-4ce4-902b-4d4ac0bf7f40/IGVFFI9573OXCH.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_exp17_rna_10x4_NGS3_rna_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0398ALPE/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI8751YQRY/"
],
"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/IGVFDS9133EBOD/",
"accession": "IGVFDS9133EBOD",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:17:43.602298+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM9149ZACE/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM9149ZACE",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf17_10x4"
],
"cellular_sub_pool": "4",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009320/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "RUES2",
"term_name": "RUES2"
}
],
"status": "released",
"summary": "multiplexed sample: RUES2 differentiated cell specimen induced to gastrula for 2 days, female, Homo sapiens; RUES2 differentiated cell specimen induced to gastrula for 1 day, female, Homo sapiens; ... and 10 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": "2025-01-27T23:29:06.116326+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "c9387380-2512-4a46-9484-e14aacbf4ea4"
}