{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5534BNMJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5534BNMJ",
"aliases": [
"maya-kasowski:sample_4232_WGS"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002117/",
"assay_slims": [
"genetic profiling"
],
"status": "released",
"term_name": "whole genome sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5534BNMJ](/measurement-sets/IGVFDS5534BNMJ/) 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/IGVFDS5534BNMJ/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM7706IRBK](/primary-cells/IGVFSM7706IRBK/) 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": "/primary-cells/IGVFSM7706IRBK/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS5534BNMJ](/measurement-sets/IGVFDS5534BNMJ/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS5534BNMJ/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7706IRBK](/primary-cells/IGVFSM7706IRBK/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM7706IRBK/"
}
]
},
"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": "2025-03-06T02:53:34.512146+00:00",
"data_use_limitation_summaries": [
"GRU"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9663VUZC/",
"accession": "IGVFDO9663VUZC",
"aliases": [
"maya-kasowski:donor_4232"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/alignment-files/IGVFFI0054IYFK/",
"accession": "IGVFFI0054IYFK",
"aliases": [
"maya-kasowski:sample_4232_WGS_bam"
],
"assembly": "GRCh38",
"content_type": "alignments",
"controlled_access": true,
"creation_timestamp": "2025-03-06T10:04:07.725028+00:00",
"file_format": "bam",
"file_size": 76208199249,
"href": "/alignment-files/IGVFFI0054IYFK/@@download/IGVFFI0054IYFK.bam",
"s3_uri": "s3://igvf-restricted-files/2025/03/06/297b22ed-20f7-4e26-a9a1-02544db8fbe2/IGVFFI0054IYFK.bam",
"status": "released",
"submitted_file_name": "/users/shouvikm/data/WGS/4232_KASWGS3/G24-3304_460a45cc-98c3-4f11-bc32-c2c46ccb00cc_24H-017MP0013_2024-01-21T08:49:31.139Z.bam",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/maya-kasowski/",
"title": "Maya Kasowski, Stanford"
},
"preferred_assay_title": "WGS",
"protocols": [
"https://www.protocols.io/view/whole-genome-sequencing-preparation-yxmvmyoq9v3p/v1"
],
"release_timestamp": "2025-03-26T19:36:56.441265+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM7706IRBK/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7706IRBK",
"aliases": [
"maya-kasowski:sample_4232"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/5d9a7abd-9957-4b1a-91cd-72ce9610785c/",
"certificate_identifier": "IP115-20",
"controlled_access": true,
"data_use_limitation": "GRU",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002371/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "bone marrow",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "Homo sapiens bone marrow cell",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/2bebcf9d-414f-4058-8d97-00020741a419/",
"title": "Shouvik Mani"
},
"submitted_files_timestamp": "2025-03-06T10:04:07.725028+00:00",
"summary": "WGS",
"uuid": "872ae3e0-0fdc-4487-bd8b-43ccdb599a9a"
}