{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4493CHDR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4493CHDR",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf13_10x2"
],
"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 [IGVFSM7106DAZZ](/multiplexed-samples/IGVFSM7106DAZZ/) has in progress subobject tabular file [IGVFFI7218IPWP](/tabular-files/IGVFFI7218IPWP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM7106DAZZ/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM7106DAZZ](/multiplexed-samples/IGVFSM7106DAZZ/) 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/IGVFSM7106DAZZ/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS2143LCWD](/auxiliary-sets/IGVFDS2143LCWD/) 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/IGVFDS2143LCWD/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4493CHDR](/measurement-sets/IGVFDS4493CHDR/) 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/IGVFDS4493CHDR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4493CHDR](/measurement-sets/IGVFDS4493CHDR/) 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/IGVFDS4493CHDR/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2143LCWD/",
"accession": "IGVFDS2143LCWD",
"aliases": [
"ansuman-satpathy:multiseq_igvf13_10x2"
],
"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": "2024-07-23T20:58:58.300965+00:00",
"data_use_limitation_summaries": [
"GRU-PUB"
],
"donors": [
{
"@id": "/human-donors/IGVFDO4204VAPA/",
"accession": "IGVFDO4204VAPA",
"aliases": [
"thomas-quertermous:LAD_multiome_donor3"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1255NCVH/",
"accession": "IGVFDO1255NCVH",
"aliases": [
"thomas-quertermous:LAD_multiome_donor2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2120EMSK/",
"accession": "IGVFDO2120EMSK",
"aliases": [
"thomas-quertermous:LAD_multiome_donor1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4556QZMA/",
"accession": "IGVFDO4556QZMA",
"aliases": [
"thomas-quertermous:LAD_multiome_donor4"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3216EBXZ/",
"accession": "IGVFFI3216EBXZ",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS1_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:24:38.436456+00:00",
"file_format": "fastq",
"file_size": 2007334565,
"href": "/sequence-files/IGVFFI3216EBXZ/@@download/IGVFFI3216EBXZ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/88acc9e2-2b92-4383-bd61-b6666381e9fb/IGVFFI3216EBXZ.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0334IHJO/",
"accession": "IGVFFI0334IHJO",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS1_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:27:01.598445+00:00",
"file_format": "fastq",
"file_size": 9179394509,
"href": "/sequence-files/IGVFFI0334IHJO/@@download/IGVFFI0334IHJO.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/63346d10-8f96-4867-9bc7-897750164772/IGVFFI0334IHJO.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L001_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9700OSNI/",
"accession": "IGVFFI9700OSNI",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS3_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:32:14.673376+00:00",
"file_format": "fastq",
"file_size": 9408007156,
"href": "/sequence-files/IGVFFI9700OSNI/@@download/IGVFFI9700OSNI.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/34a40231-da47-481a-8b94-e92fecffd028/IGVFFI9700OSNI.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8562KVTJ/",
"accession": "IGVFFI8562KVTJ",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS3_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:33:19.076244+00:00",
"file_format": "fastq",
"file_size": 5167420665,
"href": "/sequence-files/IGVFFI8562KVTJ/@@download/IGVFFI8562KVTJ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/5699cfe7-4282-4cf3-b2c8-7bf56d41f4f0/IGVFFI8562KVTJ.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2106SEWY/",
"accession": "IGVFFI2106SEWY",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS2_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:30:35.329520+00:00",
"file_format": "fastq",
"file_size": 9212857529,
"href": "/sequence-files/IGVFFI2106SEWY/@@download/IGVFFI2106SEWY.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/3a95601c-3a67-449d-ba9e-b0ab139aeb60/IGVFFI2106SEWY.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L002_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5887WXJN/",
"accession": "IGVFFI5887WXJN",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS3_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:34:17.998757+00:00",
"file_format": "fastq",
"file_size": 9219592298,
"href": "/sequence-files/IGVFFI5887WXJN/@@download/IGVFFI5887WXJN.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/cbb0742e-8979-45d1-8fbe-8d426cc81044/IGVFFI5887WXJN.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L003_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4489GXJH/",
"accession": "IGVFFI4489GXJH",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS1_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:25:13.092700+00:00",
"file_format": "fastq",
"file_size": 9371818868,
"href": "/sequence-files/IGVFFI4489GXJH/@@download/IGVFFI4489GXJH.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/0d803511-a732-4c43-8775-41f10e7dfc0a/IGVFFI4489GXJH.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8339QLVN/",
"accession": "IGVFFI8339QLVN",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS1_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:26:13.830671+00:00",
"file_format": "fastq",
"file_size": 5146496539,
"href": "/sequence-files/IGVFFI8339QLVN/@@download/IGVFFI8339QLVN.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/d591c037-093d-4b60-90d9-3ebb6e2ba8c5/IGVFFI8339QLVN.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9334SUBJ/",
"accession": "IGVFFI9334SUBJ",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS2_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:28:02.812822+00:00",
"file_format": "fastq",
"file_size": 2002397794,
"href": "/sequence-files/IGVFFI9334SUBJ/@@download/IGVFFI9334SUBJ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/400c56de-ac50-4de8-98ef-4ad508a3d7eb/IGVFFI9334SUBJ.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2797FMOI/",
"accession": "IGVFFI2797FMOI",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS2_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:28:39.971703+00:00",
"file_format": "fastq",
"file_size": 9390369517,
"href": "/sequence-files/IGVFFI2797FMOI/@@download/IGVFFI2797FMOI.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/32d227ca-d35a-4903-ac9f-fe42c0041efa/IGVFFI2797FMOI.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1753PLPI/",
"accession": "IGVFFI1753PLPI",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS2_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:29:44.425940+00:00",
"file_format": "fastq",
"file_size": 5160601420,
"href": "/sequence-files/IGVFFI1753PLPI/@@download/IGVFFI1753PLPI.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/82d860b4-9857-4f13-9777-07fb2babde0d/IGVFFI1753PLPI.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7961ZCVK/",
"accession": "IGVFFI7961ZCVK",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x2_NGS3_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:31:39.835164+00:00",
"file_format": "fastq",
"file_size": 1999737905,
"href": "/sequence-files/IGVFFI7961ZCVK/@@download/IGVFFI7961ZCVK.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/61f63cb1-6b05-4559-beab-7bef4fb7dfdb/IGVFFI7961ZCVK.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/tq_fastqs/ATAC/igvf13_s2_atac_S2_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5277KTGH/",
"accession": "IGVFFI5277KTGH",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_atac_10x2_NGS3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:33:39.505868+00:00",
"file_format": "yaml",
"file_size": 1378,
"href": "/configuration-files/IGVFFI5277KTGH/@@download/IGVFFI5277KTGH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/feb41dae-22de-48a9-a0b5-81ef6ebc8f4d/IGVFFI5277KTGH.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_atac_10x2_NGS3_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9646VVVI/",
"accession": "IGVFFI9646VVVI",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_atac_10x2_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:33:32.341434+00:00",
"file_format": "yaml",
"file_size": 1378,
"href": "/configuration-files/IGVFFI9646VVVI/@@download/IGVFFI9646VVVI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/703e08e0-0431-4d71-9873-996f59dd2421/IGVFFI9646VVVI.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_atac_10x2_NGS1_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6725RIWP/",
"accession": "IGVFFI6725RIWP",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_atac_10x2_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:33:35.842710+00:00",
"file_format": "yaml",
"file_size": 1379,
"href": "/configuration-files/IGVFFI6725RIWP/@@download/IGVFFI6725RIWP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/6048cac6-9ef9-440f-99fc-eb8af2d0d763/IGVFFI6725RIWP.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_atac_10x2_NGS2_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0226SGHL/"
],
"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/IGVFDS8398CKNT/",
"accession": "IGVFDS8398CKNT",
"status": "released"
}
],
"release_timestamp": "2025-03-22T00:40:30.434082+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7106DAZZ/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7106DAZZ",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf13_10x2"
],
"classifications": [
"tissue",
"multiplexed sample"
],
"disease_terms": [
{
"@id": "/phenotype-terms/MONDO_0005010/",
"status": "released",
"term_name": "coronary artery disorder"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/1779b95c-3032-475b-8d7a-c607a2e42d32/",
"certificate_identifier": "IP115-09",
"controlled_access": true,
"data_use_limitation": "GRU",
"data_use_limitation_modifiers": [
"PUB"
],
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0001626/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left coronary artery",
"term_name": "left coronary artery"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female, 48 years) left coronary artery tissue associated with coronary artery disorder; Homo sapiens (female, 73 years) left coronary artery tissue associated with coronary artery disorder; ... and 2 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": "2024-07-23T21:24:38.436456+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
"uuid": "203292d2-6f3b-45f7-965f-b2daff9fb7f0"
}