{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9931JAJO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9931JAJO",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1707"
],
"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 [IGVFDS9931JAJO](/measurement-sets/IGVFDS9931JAJO/) 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/IGVFDS9931JAJO/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9931JAJO](/measurement-sets/IGVFDS9931JAJO/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9931JAJO/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9931JAJO](/measurement-sets/IGVFDS9931JAJO/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9931JAJO/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM1865KZPO](/tissues/IGVFSM1865KZPO/) 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/IGVFSM1865KZPO/"
},
{
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9931JAJO](/measurement-sets/IGVFDS9931JAJO/) 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/IGVFDS9931JAJO/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1865KZPO](/tissues/IGVFSM1865KZPO/) 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/IGVFSM1865KZPO/"
}
]
},
"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": "2025-03-05T15:34:31.048451+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/IGVFFI0471SKPU/",
"accession": "IGVFFI0471SKPU",
"aliases": [
"buenrostro-bernstein:SS-LS_8320_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:49.919589+00:00",
"file_format": "fastq",
"file_size": 1821398077,
"href": "/sequence-files/IGVFFI0471SKPU/@@download/IGVFFI0471SKPU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b5581d4f-ca55-46f6-bcd1-1d6efaf5205f/IGVFFI0471SKPU.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-2166_L1_SS-PKR-584_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2080AZSU/",
"accession": "IGVFFI2080AZSU",
"aliases": [
"buenrostro-bernstein:SS-LS_8352_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:41.992678+00:00",
"file_format": "fastq",
"file_size": 682250718,
"href": "/sequence-files/IGVFFI2080AZSU/@@download/IGVFFI2080AZSU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/35f41f64-c25e-47b4-9843-a8f851e188e7/IGVFFI2080AZSU.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-2238_L8_SS-PKR-584_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0324KRDV/",
"accession": "IGVFFI0324KRDV",
"aliases": [
"buenrostro-bernstein:SS-LS_8352_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:40.166928+00:00",
"file_format": "fastq",
"file_size": 484380293,
"href": "/sequence-files/IGVFFI0324KRDV/@@download/IGVFFI0324KRDV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/18c160f9-cc7e-4b20-801a-de8f7a5e9905/IGVFFI0324KRDV.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-2238_L8_SS-PKR-584_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3897TQJB/",
"accession": "IGVFFI3897TQJB",
"aliases": [
"buenrostro-bernstein:SS-LS_8320_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:48.247225+00:00",
"file_format": "fastq",
"file_size": 1302980810,
"href": "/sequence-files/IGVFFI3897TQJB/@@download/IGVFFI3897TQJB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/1b1ca528-569a-4689-9367-a2b70889296a/IGVFFI3897TQJB.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-2166_L1_SS-PKR-584_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0456AGBL/",
"accession": "IGVFFI0456AGBL",
"aliases": [
"buenrostro-bernstein:SS-LS_8320_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:56.263149+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI0456AGBL/@@download/IGVFFI0456AGBL.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/ef12b35d-d6d5-43f4-88e5-7b8f51498c97/IGVFFI0456AGBL.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8320_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4101FQNX/",
"accession": "IGVFFI4101FQNX",
"aliases": [
"buenrostro-bernstein:SS-LS_8352_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:12.383695+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI4101FQNX/@@download/IGVFFI4101FQNX.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/4e0e5243-9f30-44f0-9471-75061ebaccaa/IGVFFI4101FQNX.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8352_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0918IHQJ/"
],
"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/IGVFDS1227FUJY/",
"accession": "IGVFDS1227FUJY",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:57.586384+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1865KZPO/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1865KZPO",
"aliases": [
"buenrostro-bernstein:BioSam 5149_SS-PKR 584"
],
"cellular_sub_pool": "SS-PKR 584",
"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 584)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:57:48.247225+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "8fae0b02-976a-481b-9228-9bbe714a89b5"
}