{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6623PZMD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6623PZMD",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1687"
],
"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 [IGVFSM7444XSMN](/tissues/IGVFSM7444XSMN/) 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/IGVFSM7444XSMN/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6623PZMD](/measurement-sets/IGVFDS6623PZMD/) 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/IGVFDS6623PZMD/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6623PZMD](/measurement-sets/IGVFDS6623PZMD/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6623PZMD/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6623PZMD](/measurement-sets/IGVFDS6623PZMD/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6623PZMD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6623PZMD](/measurement-sets/IGVFDS6623PZMD/) 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/IGVFDS6623PZMD/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM7444XSMN](/tissues/IGVFSM7444XSMN/) 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/IGVFSM7444XSMN/"
}
]
},
"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": "2025-03-05T15:34:26.767947+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO7272VQKZ/",
"accession": "IGVFDO7272VQKZ",
"aliases": [
"ali-mortazavi:770_CASTJ_10F",
"buenrostro-bernstein:Donor 2072"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7887KVTU/",
"accession": "IGVFFI7887KVTU",
"aliases": [
"buenrostro-bernstein:SS-LS_8314_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:35.732437+00:00",
"file_format": "fastq",
"file_size": 4293167335,
"href": "/sequence-files/IGVFFI7887KVTU/@@download/IGVFFI7887KVTU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/ca6f5c26-acc3-416a-a7b8-dba7653b3afd/IGVFFI7887KVTU.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-2160_L1_SS-PKR-574_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2990RHQV/",
"accession": "IGVFFI2990RHQV",
"aliases": [
"buenrostro-bernstein:SS-LS_8346_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:27.866502+00:00",
"file_format": "fastq",
"file_size": 993520272,
"href": "/sequence-files/IGVFFI2990RHQV/@@download/IGVFFI2990RHQV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/eca6677a-0b07-4a36-bb89-40dba2a61729/IGVFFI2990RHQV.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-2232_L8_SS-PKR-574_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9015IWKL/",
"accession": "IGVFFI9015IWKL",
"aliases": [
"buenrostro-bernstein:SS-LS_8314_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:33.970403+00:00",
"file_format": "fastq",
"file_size": 3081784116,
"href": "/sequence-files/IGVFFI9015IWKL/@@download/IGVFFI9015IWKL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/8093fa28-a044-4d19-a714-dec4a1fabdf0/IGVFFI9015IWKL.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-2160_L1_SS-PKR-574_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3874PDTF/",
"accession": "IGVFFI3874PDTF",
"aliases": [
"buenrostro-bernstein:SS-LS_8346_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:30.062597+00:00",
"file_format": "fastq",
"file_size": 1391768227,
"href": "/sequence-files/IGVFFI3874PDTF/@@download/IGVFFI3874PDTF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/1482ba75-e550-4a14-961a-a6bbe5dcaf58/IGVFFI3874PDTF.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-2232_L8_SS-PKR-574_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9591TFXX/",
"accession": "IGVFFI9591TFXX",
"aliases": [
"buenrostro-bernstein:SS-LS_8346_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:05.804862+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI9591TFXX/@@download/IGVFFI9591TFXX.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/842a7cf2-ff2d-4c6a-8e6c-9d97d0e580fc/IGVFFI9591TFXX.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8346_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3324IZAH/",
"accession": "IGVFFI3324IZAH",
"aliases": [
"buenrostro-bernstein:SS-LS_8314_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:50.868616+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI3324IZAH/@@download/IGVFFI3324IZAH.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/bbe4322d-9eba-4e6a-9b0c-c3683cdef572/IGVFFI3324IZAH.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8314_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9358DHKB/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI6680XCDT/",
"/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/IGVFDS0997DPPP/",
"accession": "IGVFDS0997DPPP",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:31.852024+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM7444XSMN/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7444XSMN",
"aliases": [
"buenrostro-bernstein:BioSam 5149_SS-PKR 574"
],
"cellular_sub_pool": "SS-PKR 574",
"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 574)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:57:33.970403+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "6df01172-60e1-49d1-ac8a-ed960ef5ffaa"
}