{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1681DUIN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1681DUIN",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf13_10x1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS1833OZIZ](/auxiliary-sets/IGVFDS1833OZIZ/) 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/IGVFDS1833OZIZ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1681DUIN](/measurement-sets/IGVFDS1681DUIN/) 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/IGVFDS1681DUIN/"
},
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM6422YWWA](/multiplexed-samples/IGVFSM6422YWWA/) has in progress subobject tabular file [IGVFFI7218IPWP](/tabular-files/IGVFFI7218IPWP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM6422YWWA/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM6422YWWA](/multiplexed-samples/IGVFSM6422YWWA/) 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/IGVFSM6422YWWA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1681DUIN](/measurement-sets/IGVFDS1681DUIN/) 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/IGVFDS1681DUIN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1833OZIZ/",
"accession": "IGVFDS1833OZIZ",
"aliases": [
"ansuman-satpathy:multiseq_igvf13_10x1"
],
"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": "2024-07-23T20:58:57.684381+00:00",
"data_use_limitation_summaries": [
"GRU-PUB"
],
"donors": [
{
"@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"
},
{
"@id": "/human-donors/IGVFDO1255NCVH/",
"accession": "IGVFDO1255NCVH",
"aliases": [
"thomas-quertermous:LAD_multiome_donor2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4204VAPA/",
"accession": "IGVFDO4204VAPA",
"aliases": [
"thomas-quertermous:LAD_multiome_donor3"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9872ZCYZ/",
"accession": "IGVFFI9872ZCYZ",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS1_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:16:51.157871+00:00",
"file_format": "fastq",
"file_size": 8980556187,
"href": "/sequence-files/IGVFFI9872ZCYZ/@@download/IGVFFI9872ZCYZ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/b47252f3-4495-4b29-85af-5795527d2fea/IGVFFI9872ZCYZ.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_s1_atac_S1_L001_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3017ZKLK/",
"accession": "IGVFFI3017ZKLK",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS1_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:14:25.155976+00:00",
"file_format": "fastq",
"file_size": 2029415125,
"href": "/sequence-files/IGVFFI3017ZKLK/@@download/IGVFFI3017ZKLK.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/07a5513a-c160-44ed-940d-b23324989b61/IGVFFI3017ZKLK.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_s1_atac_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3923LTFP/",
"accession": "IGVFFI3923LTFP",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS1_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:16:03.421402+00:00",
"file_format": "fastq",
"file_size": 4985554098,
"href": "/sequence-files/IGVFFI3923LTFP/@@download/IGVFFI3923LTFP.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/3278dcd3-7254-4c1c-90f9-a0ff0637b549/IGVFFI3923LTFP.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_s1_atac_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0244DQNM/",
"accession": "IGVFFI0244DQNM",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS2_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:17:53.278375+00:00",
"file_format": "fastq",
"file_size": 2029645422,
"href": "/sequence-files/IGVFFI0244DQNM/@@download/IGVFFI0244DQNM.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/ee246021-e989-4627-900a-7c81ee49aa82/IGVFFI0244DQNM.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_s1_atac_S1_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9734XMHY/",
"accession": "IGVFFI9734XMHY",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS3_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:21:15.932462+00:00",
"file_format": "fastq",
"file_size": 2025108792,
"href": "/sequence-files/IGVFFI9734XMHY/@@download/IGVFFI9734XMHY.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/7651272e-695e-4687-a31f-8044647b8b17/IGVFFI9734XMHY.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_s1_atac_S1_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3455XARV/",
"accession": "IGVFFI3455XARV",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS2_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:18:28.180334+00:00",
"file_format": "fastq",
"file_size": 9175613525,
"href": "/sequence-files/IGVFFI3455XARV/@@download/IGVFFI3455XARV.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/368c87cf-269d-450c-afe0-bd524c0f2fae/IGVFFI3455XARV.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_s1_atac_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8922GVCO/",
"accession": "IGVFFI8922GVCO",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS3_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:22:52.593382+00:00",
"file_format": "fastq",
"file_size": 5005023234,
"href": "/sequence-files/IGVFFI8922GVCO/@@download/IGVFFI8922GVCO.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/f18b8adb-6e1f-459b-81bf-bdd53f8ccc5b/IGVFFI8922GVCO.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_s1_atac_S1_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8899OCMF/",
"accession": "IGVFFI8899OCMF",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS1_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:15:02.604449+00:00",
"file_format": "fastq",
"file_size": 9156412521,
"href": "/sequence-files/IGVFFI8899OCMF/@@download/IGVFFI8899OCMF.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/8d16cdcf-e0e5-4c93-83c5-190575230a31/IGVFFI8899OCMF.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_s1_atac_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9768MFHS/",
"accession": "IGVFFI9768MFHS",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS3_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:21:50.967724+00:00",
"file_format": "fastq",
"file_size": 9184493464,
"href": "/sequence-files/IGVFFI9768MFHS/@@download/IGVFFI9768MFHS.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/d6f30aad-963b-41ef-941d-2cdd097b415f/IGVFFI9768MFHS.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_s1_atac_S1_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9561YTLI/",
"accession": "IGVFFI9561YTLI",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS2_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:19:30.856600+00:00",
"file_format": "fastq",
"file_size": 5001512855,
"href": "/sequence-files/IGVFFI9561YTLI/@@download/IGVFFI9561YTLI.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/3ec4f792-6b38-4e6d-948c-5a3ae40907ec/IGVFFI9561YTLI.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_s1_atac_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8966HZNP/",
"accession": "IGVFFI8966HZNP",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS2_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:20:15.422956+00:00",
"file_format": "fastq",
"file_size": 9014198415,
"href": "/sequence-files/IGVFFI8966HZNP/@@download/IGVFFI8966HZNP.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/bc3a6134-f5c8-4d04-a8dc-f270837aef34/IGVFFI8966HZNP.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_s1_atac_S1_L002_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6086MFMD/",
"accession": "IGVFFI6086MFMD",
"aliases": [
"ansuman-satpathy:igvf_exp13_atac_10x1_NGS3_r3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:23:38.786658+00:00",
"file_format": "fastq",
"file_size": 9012642292,
"href": "/sequence-files/IGVFFI6086MFMD/@@download/IGVFFI6086MFMD.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/7aa2cce7-8538-4831-8567-1e4cb9edf0e7/IGVFFI6086MFMD.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_s1_atac_S1_L003_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7307TRXS/",
"accession": "IGVFFI7307TRXS",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_atac_10x1_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:33:20.303207+00:00",
"file_format": "yaml",
"file_size": 1377,
"href": "/configuration-files/IGVFFI7307TRXS/@@download/IGVFFI7307TRXS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/2bc248ce-c4e9-46a5-b4c7-0172fc7fe3e8/IGVFFI7307TRXS.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_atac_10x1_NGS1_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3285XVSJ/",
"accession": "IGVFFI3285XVSJ",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_atac_10x1_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:33:24.285074+00:00",
"file_format": "yaml",
"file_size": 1378,
"href": "/configuration-files/IGVFFI3285XVSJ/@@download/IGVFFI3285XVSJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/11bb7d9d-dd59-4100-b526-cafa93a3a625/IGVFFI3285XVSJ.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_atac_10x1_NGS2_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4759YEZJ/",
"accession": "IGVFFI4759YEZJ",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_atac_10x1_NGS3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:33:28.229894+00:00",
"file_format": "yaml",
"file_size": 1375,
"href": "/configuration-files/IGVFFI4759YEZJ/@@download/IGVFFI4759YEZJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/b9c09d97-ac63-4e9e-bf01-b0092bff0601/IGVFFI4759YEZJ.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_atac_10x1_NGS3_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5901DVUG/"
],
"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/IGVFDS3842BVTL/",
"accession": "IGVFDS3842BVTL",
"status": "released"
}
],
"release_timestamp": "2025-03-22T00:40:21.958540+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM6422YWWA/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM6422YWWA",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf13_10x1"
],
"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": "2024-07-23T21:14:25.155976+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
"uuid": "b257a97c-cb7a-4da1-a760-7e014412900d"
}