{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9953SCFR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9953SCFR",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1551"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9953SCFR](/measurement-sets/IGVFDS9953SCFR/) 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/IGVFDS9953SCFR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9953SCFR](/measurement-sets/IGVFDS9953SCFR/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9953SCFR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9953SCFR](/measurement-sets/IGVFDS9953SCFR/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9953SCFR/"
},
{
"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 [IGVFSM0205CCTB](/tissues/IGVFSM0205CCTB/) 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/IGVFSM0205CCTB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9953SCFR](/measurement-sets/IGVFDS9953SCFR/) 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/IGVFDS9953SCFR/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM0205CCTB](/tissues/IGVFSM0205CCTB/) 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/IGVFSM0205CCTB/"
}
]
},
"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": "2025-03-05T15:33:42.684317+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO0972REDW/",
"accession": "IGVFDO0972REDW",
"aliases": [
"ali-mortazavi:767_B6J_10M",
"buenrostro-bernstein:Donor 2075"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7078IVCN/",
"accession": "IGVFFI7078IVCN",
"aliases": [
"buenrostro-bernstein:SS-LS_8340_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:53:14.580553+00:00",
"file_format": "fastq",
"file_size": 2778988058,
"href": "/sequence-files/IGVFFI7078IVCN/@@download/IGVFFI7078IVCN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/cd084b2c-ee6c-4b29-a956-37196db48826/IGVFFI7078IVCN.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-2226_L8_SS-PKR-530_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6362BVFD/",
"accession": "IGVFFI6362BVFD",
"aliases": [
"buenrostro-bernstein:SS-LS_8276_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:22.089844+00:00",
"file_format": "fastq",
"file_size": 4098650374,
"href": "/sequence-files/IGVFFI6362BVFD/@@download/IGVFFI6362BVFD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/c44cd0bb-9283-43cf-9cc3-9c9774905a1b/IGVFFI6362BVFD.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-2154_L2_SS-PKR-530_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2584APXB/",
"accession": "IGVFFI2584APXB",
"aliases": [
"buenrostro-bernstein:SS-LS_8340_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:53:16.638468+00:00",
"file_format": "fastq",
"file_size": 3882483694,
"href": "/sequence-files/IGVFFI2584APXB/@@download/IGVFFI2584APXB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4f6128f5-3110-490c-988d-8bfa78b5dbe2/IGVFFI2584APXB.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-2226_L8_SS-PKR-530_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2665IMRB/",
"accession": "IGVFFI2665IMRB",
"aliases": [
"buenrostro-bernstein:SS-LS_8276_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:23.569348+00:00",
"file_format": "fastq",
"file_size": 5806670496,
"href": "/sequence-files/IGVFFI2665IMRB/@@download/IGVFFI2665IMRB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b3ef7aef-04f5-453b-9a7e-02042a961ae0/IGVFFI2665IMRB.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-2154_L2_SS-PKR-530_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0367VOEG/",
"accession": "IGVFFI0367VOEG",
"aliases": [
"buenrostro-bernstein:SS-LS_8340_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:40.332056+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI0367VOEG/@@download/IGVFFI0367VOEG.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/9c0dc23d-b1de-4043-a584-70f70c75d15c/IGVFFI0367VOEG.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8340_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1601ZCGP/",
"accession": "IGVFFI1601ZCGP",
"aliases": [
"buenrostro-bernstein:SS-LS_8276_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:25.338519+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI1601ZCGP/@@download/IGVFFI1601ZCGP.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/ba4a7477-b34a-455d-af8f-e6ac386df2e9/IGVFFI1601ZCGP.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8276_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2638VMPJ/"
],
"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/IGVFDS9664UTZY/",
"accession": "IGVFDS9664UTZY",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:48.137375+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM0205CCTB/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0205CCTB",
"aliases": [
"buenrostro-bernstein:BioSam 5152_SS-PKR 530"
],
"cellular_sub_pool": "SS-PKR 530",
"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 C57BL/6J (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 530)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:52:22.089844+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "98ea35ee-7c3e-4b83-81c1-52d1ea3bc73e"
}