{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8398CKNT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8398CKNT",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf13_10x2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"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 [IGVFDS8398CKNT](/measurement-sets/IGVFDS8398CKNT/) 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/IGVFDS8398CKNT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8398CKNT](/measurement-sets/IGVFDS8398CKNT/) 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/IGVFDS8398CKNT/"
}
]
},
"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": "2024-07-23T20:58:57.991453+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/IGVFFI0500KQFG/",
"accession": "IGVFFI0500KQFG",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS2_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:29:02.627635+00:00",
"file_format": "fastq",
"file_size": 6644622665,
"href": "/sequence-files/IGVFFI0500KQFG/@@download/IGVFFI0500KQFG.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/ddfa8bbd-b90f-4149-a46c-a36aef8526b2/IGVFFI0500KQFG.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1190HHMC/",
"accession": "IGVFFI1190HHMC",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS1_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:25:39.944438+00:00",
"file_format": "fastq",
"file_size": 6621706666,
"href": "/sequence-files/IGVFFI1190HHMC/@@download/IGVFFI1190HHMC.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/4e3fba8b-4cb9-4b03-8d1b-e4168372b37e/IGVFFI1190HHMC.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1136TUAK/",
"accession": "IGVFFI1136TUAK",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS1_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:26:48.678398+00:00",
"file_format": "fastq",
"file_size": 14688776063,
"href": "/sequence-files/IGVFFI1136TUAK/@@download/IGVFFI1136TUAK.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/95ead02f-498d-467f-bd25-179d9b32fd03/IGVFFI1136TUAK.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6355OMRZ/",
"accession": "IGVFFI6355OMRZ",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS1_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:24:52.868380+00:00",
"file_format": "fastq",
"file_size": 1772094419,
"href": "/sequence-files/IGVFFI6355OMRZ/@@download/IGVFFI6355OMRZ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/14a49fa7-3028-4fc0-b03e-ed792b9b41c3/IGVFFI6355OMRZ.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2573YKMX/",
"accession": "IGVFFI2573YKMX",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS1_i2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:25:08.549554+00:00",
"file_format": "fastq",
"file_size": 1878471946,
"href": "/sequence-files/IGVFFI2573YKMX/@@download/IGVFFI2573YKMX.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/bbeaa847-332c-42dc-8bcb-bad2d46d489e/IGVFFI2573YKMX.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1429UDGT/",
"accession": "IGVFFI1429UDGT",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS2_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:28:14.918010+00:00",
"file_format": "fastq",
"file_size": 1740648939,
"href": "/sequence-files/IGVFFI1429UDGT/@@download/IGVFFI1429UDGT.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/42a24c33-2753-4518-b424-7ffb057c6161/IGVFFI1429UDGT.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5562QBAP/",
"accession": "IGVFFI5562QBAP",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS2_i2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:28:34.313134+00:00",
"file_format": "fastq",
"file_size": 1856492248,
"href": "/sequence-files/IGVFFI5562QBAP/@@download/IGVFFI5562QBAP.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/398ffb00-b756-473e-88c4-eac8e83c6cfc/IGVFFI5562QBAP.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5686HDAC/",
"accession": "IGVFFI5686HDAC",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS2_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:30:12.168601+00:00",
"file_format": "fastq",
"file_size": 14777438113,
"href": "/sequence-files/IGVFFI5686HDAC/@@download/IGVFFI5686HDAC.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/8625951b-526f-4658-9ff3-1c172f313efb/IGVFFI5686HDAC.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2960RIPL/",
"accession": "IGVFFI2960RIPL",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS3_r1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:32:20.744001+00:00",
"file_format": "fastq",
"file_size": 6641371312,
"href": "/sequence-files/IGVFFI2960RIPL/@@download/IGVFFI2960RIPL.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/d05b4ea5-9b9d-433b-bf8b-e7268d20be63/IGVFFI2960RIPL.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6516ODEU/",
"accession": "IGVFFI6516ODEU",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS3_i1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:31:35.108912+00:00",
"file_format": "fastq",
"file_size": 1741224251,
"href": "/sequence-files/IGVFFI6516ODEU/@@download/IGVFFI6516ODEU.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/bbb5dabc-4b13-462d-9ceb-2390682957b3/IGVFFI6516ODEU.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5906XPBY/",
"accession": "IGVFFI5906XPBY",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS3_i2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:31:54.457073+00:00",
"file_format": "fastq",
"file_size": 1863734377,
"href": "/sequence-files/IGVFFI5906XPBY/@@download/IGVFFI5906XPBY.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/ae7c9370-6eca-4cb9-8252-3afef86a0173/IGVFFI5906XPBY.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L003_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6623FYZW/",
"accession": "IGVFFI6623FYZW",
"aliases": [
"ansuman-satpathy:igvf_exp13_rna_10x2_NGS3_r2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2024-07-23T21:33:37.999645+00:00",
"file_format": "fastq",
"file_size": 14716782065,
"href": "/sequence-files/IGVFFI6623FYZW/@@download/IGVFFI6623FYZW.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2024/07/23/ffe32c39-d250-4f0b-ab9e-4b82f1b7e07e/IGVFFI6623FYZW.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_IGVF13_McGinnis/GEX/FASTQ/igvf13_s2_rna_S2_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8937AWCM/",
"accession": "IGVFFI8937AWCM",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_rna_10x2_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:35:04.080580+00:00",
"file_format": "yaml",
"file_size": 1394,
"href": "/configuration-files/IGVFFI8937AWCM/@@download/IGVFFI8937AWCM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/4404494b-e783-4b5b-bd2c-479d90ef44b4/IGVFFI8937AWCM.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_rna_10x2_NGS1_rna_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3096BEXO/",
"accession": "IGVFFI3096BEXO",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_rna_10x2_NGS3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:35:11.339481+00:00",
"file_format": "yaml",
"file_size": 1396,
"href": "/configuration-files/IGVFFI3096BEXO/@@download/IGVFFI3096BEXO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/3f01352f-c8e6-4a35-93c0-2ffd3307e2a2/IGVFFI3096BEXO.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_rna_10x2_NGS3_rna_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7469SOJW/",
"accession": "IGVFFI7469SOJW",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp13_rna_10x2_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:35:07.659505+00:00",
"file_format": "yaml",
"file_size": 1395,
"href": "/configuration-files/IGVFFI7469SOJW/@@download/IGVFFI7469SOJW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/65b38f6c-8fd9-45e1-b1fc-cb1b05d807e5/IGVFFI7469SOJW.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp13_rna_10x2_NGS2_rna_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/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/IGVFDS4493CHDR/",
"accession": "IGVFDS4493CHDR",
"status": "released"
}
],
"release_timestamp": "2025-03-22T00:40:12.668286+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": "2024-07-23T21:24:52.868380+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "e5934c87-8f5d-49fc-a3fa-6f4f94bf7a25"
}