{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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],
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"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
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{
"category": "missing publication",
"detail": "Tissue [IGVFSM9059AKNM](/tissues/IGVFSM9059AKNM/) 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": "/tissues/IGVFSM9059AKNM/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0412WLCW](/measurement-sets/IGVFDS0412WLCW/) 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/IGVFDS0412WLCW/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000646](/sample-terms/NTR_0000646/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000646/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0412WLCW](/measurement-sets/IGVFDS0412WLCW/) 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/IGVFDS0412WLCW/"
}
]
},
"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": "2024-07-23T00:43:21.826987+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO5114NYSN/",
"accession": "IGVFDO5114NYSN",
"aliases": [
"ansuman-satpathy:102_CASTJ_10F"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9476EXNQ/",
"accession": "IGVFFI9476EXNQ",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_102_atac_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T04:00:32.745444+00:00",
"file_format": "fastq",
"file_size": 3420766901,
"href": "/sequence-files/IGVFFI9476EXNQ/@@download/IGVFFI9476EXNQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/5107a53e-07fb-4e00-85b5-fc5a7df5db63/IGVFFI9476EXNQ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/ATAC/ATAC_102_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8292SITB/",
"accession": "IGVFFI8292SITB",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_102_atac_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T04:04:51.258373+00:00",
"file_format": "fastq",
"file_size": 25683500731,
"href": "/sequence-files/IGVFFI8292SITB/@@download/IGVFFI8292SITB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/de69f6b1-53e5-4fc2-b927-e3c21d118e3c/IGVFFI8292SITB.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/ATAC/ATAC_102_S2_L001_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1860TEYU/",
"accession": "IGVFFI1860TEYU",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_102_atac_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T04:01:36.529797+00:00",
"file_format": "fastq",
"file_size": 24955423173,
"href": "/sequence-files/IGVFFI1860TEYU/@@download/IGVFFI1860TEYU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/84f9c722-72e6-45fb-9b80-28d5efe559ff/IGVFFI1860TEYU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/ATAC/ATAC_102_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2327RETF/",
"accession": "IGVFFI2327RETF",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_102_atac_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T04:03:31.724523+00:00",
"file_format": "fastq",
"file_size": 8262447684,
"href": "/sequence-files/IGVFFI2327RETF/@@download/IGVFFI2327RETF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/da434116-3cc3-4d65-93b9-371cfefe4454/IGVFFI2327RETF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/ATAC/ATAC_102_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7052NJFS/",
"accession": "IGVFFI7052NJFS",
"aliases": [
"ansuman-satpathy:seqspec_igvf_mouse_bridge_102_atac"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:45:32.230495+00:00",
"file_format": "yaml",
"file_size": 1382,
"href": "/configuration-files/IGVFFI7052NJFS/@@download/IGVFFI7052NJFS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/861765e2-e6da-468f-a82e-be59f2b1d4e1/IGVFFI7052NJFS.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_mouse_bridge_102_atac_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5230RAFR/",
"/analysis-sets/IGVFDS5717EBEY/",
"/analysis-sets/IGVFDS6347FMLT/"
],
"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",
"protocols": [
"https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-atac-se-ewov1nm2kgr2/v1"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS7477NVAD/",
"accession": "IGVFDS7477NVAD",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:18:34.855681+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9059AKNM/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9059AKNM",
"aliases": [
"ansuman-satpathy:102_CASTJ_10F_left_cortex"
],
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
"term_name": "left cerebral cortex"
}
],
"status": "released",
"summary": "Mus musculus CAST/EiJ (female, 10 weeks) left cerebral cortex tissue",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-23T04:00:32.745444+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "05bfc7ad-25ea-48c3-b705-03ab01ab3ea9"
}