{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9742DJVE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9742DJVE",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1546"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"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 [IGVFSM6095NJDT](/tissues/IGVFSM6095NJDT/) 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/IGVFSM6095NJDT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9742DJVE](/measurement-sets/IGVFDS9742DJVE/) 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/IGVFDS9742DJVE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9742DJVE](/measurement-sets/IGVFDS9742DJVE/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9742DJVE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9742DJVE](/measurement-sets/IGVFDS9742DJVE/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9742DJVE/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9742DJVE](/measurement-sets/IGVFDS9742DJVE/) 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/IGVFDS9742DJVE/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6095NJDT](/tissues/IGVFSM6095NJDT/) 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": "/tissues/IGVFSM6095NJDT/"
}
]
},
"award": {
"@id": "/awards/HG011986/",
"component": "mapping",
"contact_pi": {
"@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
"title": "Jason Buenrostro"
},
"title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
},
"control_for": [],
"creation_timestamp": "2025-03-05T15:34:18.379636+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO2374RRPN/",
"accession": "IGVFDO2374RRPN",
"aliases": [
"ali-mortazavi:772_CASTJ_10F",
"buenrostro-bernstein:Donor 2074"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI0194DMKY/",
"accession": "IGVFFI0194DMKY",
"aliases": [
"buenrostro-bernstein:SS-LS_8337_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:10.599984+00:00",
"file_format": "fastq",
"file_size": 1933199930,
"href": "/sequence-files/IGVFFI0194DMKY/@@download/IGVFFI0194DMKY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f7e4e53a-3b19-46d8-af6b-d72e2113e973/IGVFFI0194DMKY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2223_L8_SS-PKR-528_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7798IXDZ/",
"accession": "IGVFFI7798IXDZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8273_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:00.941264+00:00",
"file_format": "fastq",
"file_size": 3220050001,
"href": "/sequence-files/IGVFFI7798IXDZ/@@download/IGVFFI7798IXDZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/627628ae-2708-44ab-b712-b35e17a6f23e/IGVFFI7798IXDZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2151_L2_SS-PKR-528_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4753SCVM/",
"accession": "IGVFFI4753SCVM",
"aliases": [
"buenrostro-bernstein:SS-LS_8337_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:12.604081+00:00",
"file_format": "fastq",
"file_size": 2350134033,
"href": "/sequence-files/IGVFFI4753SCVM/@@download/IGVFFI4753SCVM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/a34f7e9e-f344-4a35-94e1-fc7c9029fc37/IGVFFI4753SCVM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2223_L8_SS-PKR-528_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5013NBDP/",
"accession": "IGVFFI5013NBDP",
"aliases": [
"buenrostro-bernstein:SS-LS_8273_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:59.050173+00:00",
"file_format": "fastq",
"file_size": 2492170137,
"href": "/sequence-files/IGVFFI5013NBDP/@@download/IGVFFI5013NBDP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6eec1783-a3b5-4d03-846b-f35a51957da8/IGVFFI5013NBDP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2151_L2_SS-PKR-528_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5213EZJR/",
"accession": "IGVFFI5213EZJR",
"aliases": [
"buenrostro-bernstein:SS-LS_8337_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:58.494186+00:00",
"file_format": "yaml",
"file_size": 1249,
"href": "/configuration-files/IGVFFI5213EZJR/@@download/IGVFFI5213EZJR.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/466b6d04-5255-4008-9889-3ef4c2cea220/IGVFFI5213EZJR.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8337_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1882PRIW/",
"accession": "IGVFFI1882PRIW",
"aliases": [
"buenrostro-bernstein:SS-LS_8273_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:42.616027+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI1882PRIW/@@download/IGVFFI1882PRIW.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/5a72f85c-0c7a-4581-89ab-b67d3271f182/IGVFFI1882PRIW.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8273_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5668LOCH/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI3897QKNI/",
"/tabular-files/IGVFFI2668ZFEB/"
],
"onlist_method": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS0618QCGG/",
"accession": "IGVFDS0618QCGG",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:39.909599+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6095NJDT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6095NJDT",
"aliases": [
"buenrostro-bernstein:BioSam 5151_SS-PKR 528"
],
"cellular_sub_pool": "SS-PKR 528",
"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) left cerebral cortex tissue (cellular sub pool: SS-PKR 528)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:56:59.050173+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "5b31df3a-e016-4924-957f-eb387ba57dbe"
}