{
"@context": "/terms/",
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"FileSet",
"Item"
],
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],
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],
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},
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{
"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/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM2776DDRF](/tissues/IGVFSM2776DDRF/) 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/IGVFSM2776DDRF/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6819TPGN](/measurement-sets/IGVFDS6819TPGN/) 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/IGVFDS6819TPGN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6819TPGN](/measurement-sets/IGVFDS6819TPGN/) 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/IGVFDS6819TPGN/"
}
]
},
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"component": "mapping",
"contact_pi": {
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"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
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"creation_timestamp": "2024-07-23T00:43:21.192601+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO2440QVYB/",
"accession": "IGVFDO2440QVYB",
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],
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"strain_background": "CAST/EiJ (CAST)",
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}
],
"externally_hosted": false,
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{
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"accession": "IGVFFI0814SBBP",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_101_atac_r2"
],
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"creation_timestamp": "2024-07-23T03:58:13.968180+00:00",
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8084WUEK/",
"accession": "IGVFFI8084WUEK",
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"ansuman-satpathy:igvf_mouse_bridge_101_atac_r3"
],
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"controlled_access": false,
"creation_timestamp": "2024-07-23T03:59:16.548769+00:00",
"file_format": "fastq",
"file_size": 18544112622,
"href": "/sequence-files/IGVFFI8084WUEK/@@download/IGVFFI8084WUEK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/29f1d2f0-adf1-4d3d-b8c4-ebcfd0e2fc35/IGVFFI8084WUEK.fastq.gz",
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"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3352IPEU/",
"accession": "IGVFFI3352IPEU",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_101_atac_i1"
],
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"controlled_access": false,
"creation_timestamp": "2024-07-23T02:07:32.469726+00:00",
"file_format": "fastq",
"file_size": 2458430361,
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"s3_uri": "s3://igvf-files/2024/07/23/27d0b344-96cf-4f34-9434-1876d4464b72/IGVFFI3352IPEU.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
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"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/ATAC/ATAC_101_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0305RRIM/",
"accession": "IGVFFI0305RRIM",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_101_atac_r1"
],
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"controlled_access": false,
"creation_timestamp": "2024-07-23T02:08:39.313094+00:00",
"file_format": "fastq",
"file_size": 18149966934,
"href": "/sequence-files/IGVFFI0305RRIM/@@download/IGVFFI0305RRIM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/1e0e0c7c-6bba-4461-91e0-de580fcc9500/IGVFFI0305RRIM.fastq.gz",
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"status": "released",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6533YMOZ/",
"accession": "IGVFFI6533YMOZ",
"aliases": [
"ansuman-satpathy:seqspec_igvf_mouse_bridge_101_atac"
],
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"creation_timestamp": "2024-09-18T02:45:25.181308+00:00",
"file_format": "yaml",
"file_size": 1382,
"href": "/configuration-files/IGVFFI6533YMOZ/@@download/IGVFFI6533YMOZ.yaml.gz",
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"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_mouse_bridge_101_atac_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5230RAFR/",
"/analysis-sets/IGVFDS5717EBEY/",
"/analysis-sets/IGVFDS7529ZWPQ/"
],
"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/IGVFDS9624INNM/",
"accession": "IGVFDS9624INNM",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:18:29.807217+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM2776DDRF/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2776DDRF",
"aliases": [
"ansuman-satpathy:101_CASTJ_10M_left_cortex"
],
"classifications": [
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],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
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}
],
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}
],
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"submitted_by": {
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"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "e2fc223e-77b0-417d-8ae7-a3b5a7576f0f"
}