{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1647SMVR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1647SMVR",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1785"
],
"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": "Tissue [IGVFSM0974PFBP](/tissues/IGVFSM0974PFBP/) 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/IGVFSM0974PFBP/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1647SMVR](/measurement-sets/IGVFDS1647SMVR/) 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/IGVFDS1647SMVR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1647SMVR](/measurement-sets/IGVFDS1647SMVR/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1647SMVR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1647SMVR](/measurement-sets/IGVFDS1647SMVR/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1647SMVR/"
},
{
"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 [IGVFDS1647SMVR](/measurement-sets/IGVFDS1647SMVR/) 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/IGVFDS1647SMVR/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM0974PFBP](/tissues/IGVFSM0974PFBP/) 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/IGVFSM0974PFBP/"
}
]
},
"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": "2025-03-05T15:34:44.179277+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO8443MWJY/",
"accession": "IGVFDO8443MWJY",
"aliases": [
"ali-mortazavi:773_CASTJ_10M",
"buenrostro-bernstein:Donor 2071"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI0899FVIN/",
"accession": "IGVFFI0899FVIN",
"aliases": [
"buenrostro-bernstein:SS-LS_8388_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:58.412398+00:00",
"file_format": "fastq",
"file_size": 2683829705,
"href": "/sequence-files/IGVFFI0899FVIN/@@download/IGVFFI0899FVIN.fastq.gz",
"md5sum": "006212c4e0334a356a29e5a77d267cfa",
"s3_uri": "s3://igvf-files/2025/03/05/ecd461f0-cdea-47fd-ba5f-dbe974b7a9b4/IGVFFI0899FVIN.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-2258_L5_SS-PKR-607_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1261PUUU/",
"accession": "IGVFFI1261PUUU",
"aliases": [
"buenrostro-bernstein:SS-LS_8398_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:23.794918+00:00",
"file_format": "fastq",
"file_size": 3708082474,
"href": "/sequence-files/IGVFFI1261PUUU/@@download/IGVFFI1261PUUU.fastq.gz",
"md5sum": "51f3c5b6e4304db9eb16c5ea726b81af",
"s3_uri": "s3://igvf-files/2025/03/05/cc1e99e5-ebcd-45ef-9689-5eba3547b923/IGVFFI1261PUUU.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2258_L6_SS-PKR-607_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2265QSXJ/",
"accession": "IGVFFI2265QSXJ",
"aliases": [
"buenrostro-bernstein:SS-LS_8378_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:37.525606+00:00",
"file_format": "fastq",
"file_size": 2693185973,
"href": "/sequence-files/IGVFFI2265QSXJ/@@download/IGVFFI2265QSXJ.fastq.gz",
"md5sum": "9b1b6ed530116fd98038a9b774735fc5",
"s3_uri": "s3://igvf-files/2025/03/05/c7e5a24b-7301-4be7-aff2-9551a8cb134b/IGVFFI2265QSXJ.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-2258_L4_SS-PKR-607_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0976SXNI/",
"accession": "IGVFFI0976SXNI",
"aliases": [
"buenrostro-bernstein:SS-LS_8388_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:00.621686+00:00",
"file_format": "fastq",
"file_size": 3708259655,
"href": "/sequence-files/IGVFFI0976SXNI/@@download/IGVFFI0976SXNI.fastq.gz",
"md5sum": "3e6166727a80e8d06fab36afa3da392d",
"s3_uri": "s3://igvf-files/2025/03/05/315f161e-6fd9-435b-9832-2e76624cabbd/IGVFFI0976SXNI.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-2258_L5_SS-PKR-607_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8034TOUO/",
"accession": "IGVFFI8034TOUO",
"aliases": [
"buenrostro-bernstein:SS-LS_8398_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:21.255819+00:00",
"file_format": "fastq",
"file_size": 2683112444,
"href": "/sequence-files/IGVFFI8034TOUO/@@download/IGVFFI8034TOUO.fastq.gz",
"md5sum": "989357f6a667ab8806015043e50e65a5",
"s3_uri": "s3://igvf-files/2025/03/05/23e6f570-4e2a-4b34-85b4-b6acb4a133f3/IGVFFI8034TOUO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2258_L6_SS-PKR-607_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4990PYOK/",
"accession": "IGVFFI4990PYOK",
"aliases": [
"buenrostro-bernstein:SS-LS_8378_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:39.263820+00:00",
"file_format": "fastq",
"file_size": 3741635999,
"href": "/sequence-files/IGVFFI4990PYOK/@@download/IGVFFI4990PYOK.fastq.gz",
"md5sum": "143385486c0ae3af672b32897c8b8b84",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2258_L4_SS-PKR-607_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5209XGRR/",
"accession": "IGVFFI5209XGRR",
"aliases": [
"buenrostro-bernstein:SS-LS_8388_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:33.660208+00:00",
"file_format": "yaml",
"file_size": 1248,
"href": "/configuration-files/IGVFFI5209XGRR/@@download/IGVFFI5209XGRR.yaml.gz",
"md5sum": "434b7784091d96eafac3faf0f10c7f4f",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8388_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9903ZCFP/",
"accession": "IGVFFI9903ZCFP",
"aliases": [
"buenrostro-bernstein:SS-LS_8398_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:43.144213+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI9903ZCFP/@@download/IGVFFI9903ZCFP.yaml.gz",
"md5sum": "0ce78a24958fc392b719218a48ec8be0",
"s3_uri": "s3://igvf-files/2025/03/07/6baa4300-6ced-47fb-8528-81b6f691375f/IGVFFI9903ZCFP.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8398_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3535MGCS/",
"accession": "IGVFFI3535MGCS",
"aliases": [
"buenrostro-bernstein:SS-LS_8378_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:21.809777+00:00",
"file_format": "yaml",
"file_size": 1253,
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"md5sum": "c02aea9cd11e27d6e068655894acd94d",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8378_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1893AKSY/"
],
"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/IGVFDS9449UYYC/",
"accession": "IGVFDS9449UYYC",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:13.625477+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM0974PFBP/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0974PFBP",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 607"
],
"cellular_sub_pool": "SS-PKR 607",
"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 (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 607)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:59:37.525606+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "9c155c7c-56eb-41f3-a7db-42c04bdd442f"
}