{
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"FileSet",
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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 [IGVFSM5654SLCG](/tissues/IGVFSM5654SLCG/) 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/IGVFSM5654SLCG/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2289SZHO](/measurement-sets/IGVFDS2289SZHO/) 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/IGVFDS2289SZHO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS2289SZHO](/measurement-sets/IGVFDS2289SZHO/) 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/IGVFDS2289SZHO/"
}
]
},
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"component": "mapping",
"contact_pi": {
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"title": "Ansuman Satpathy"
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"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
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"creation_timestamp": "2025-01-15T23:45:04.702721+00:00",
"donors": [
{
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],
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"status": "released",
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}
],
"externally_hosted": false,
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{
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],
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"creation_timestamp": "2025-01-15T23:50:03.873661+00:00",
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"term_name": "Illumina NovaSeq X"
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},
{
"@id": "/sequence-files/IGVFFI7536FOCA/",
"accession": "IGVFFI7536FOCA",
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],
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"creation_timestamp": "2025-01-15T23:50:27.826501+00:00",
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"href": "/sequence-files/IGVFFI7536FOCA/@@download/IGVFFI7536FOCA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/15/c0992d4e-7da5-40ad-b988-12c1b9dd26df/IGVFFI7536FOCA.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3738RLGC/",
"accession": "IGVFFI3738RLGC",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-15T23:52:07.225458+00:00",
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"file_size": 10977084189,
"href": "/sequence-files/IGVFFI3738RLGC/@@download/IGVFFI3738RLGC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/15/b2859f53-a7ea-4c7d-8659-1218059fc35b/IGVFFI3738RLGC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
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"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/bridge_new/IGVF_ATAC_775_CASTJ_10M_21_S3_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0430XHJG/",
"accession": "IGVFFI0430XHJG",
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"ansuman-satpathy:igvf_mouse_bridge_775_atac_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-15T23:53:06.671166+00:00",
"file_format": "fastq",
"file_size": 19915656345,
"href": "/sequence-files/IGVFFI0430XHJG/@@download/IGVFFI0430XHJG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/15/27315877-c771-4537-9450-bb6e4cb15542/IGVFFI0430XHJG.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq X"
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"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/bridge_new/IGVF_ATAC_775_CASTJ_10M_21_S3_L002_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6450AURM/",
"accession": "IGVFFI6450AURM",
"aliases": [
"ansuman-satpathy:seqspec_igvf_mouse_bridge_775_atac"
],
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"creation_timestamp": "2025-02-26T00:56:50.064080+00:00",
"file_format": "yaml",
"file_size": 1380,
"href": "/configuration-files/IGVFFI6450AURM/@@download/IGVFFI6450AURM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/02/26/dcf44b24-47d6-4503-972b-556d52ce4aaf/IGVFFI6450AURM.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_mouse_bridge_775_atac_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8343PSUS/",
"/analysis-sets/IGVFDS8327CWJR/"
],
"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/IGVFDS0602EDSF/",
"accession": "IGVFDS0602EDSF",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:19:08.282618+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM5654SLCG/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5654SLCG",
"aliases": [
"ansuman-satpathy:775_CASTJ_10M_left_cortex"
],
"classifications": [
"tissue"
],
"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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"status": "released",
"submitted_by": {
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"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "3b954326-a542-47e8-ba36-1702840feaf4"
}