{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6781RGTM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6781RGTM",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1779"
],
"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": "Measurement set [IGVFDS6781RGTM](/measurement-sets/IGVFDS6781RGTM/) 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/IGVFDS6781RGTM/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6781RGTM](/measurement-sets/IGVFDS6781RGTM/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6781RGTM/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6781RGTM](/measurement-sets/IGVFDS6781RGTM/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6781RGTM/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM6880XEAH](/tissues/IGVFSM6880XEAH/) 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/IGVFSM6880XEAH/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6781RGTM](/measurement-sets/IGVFDS6781RGTM/) 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/IGVFDS6781RGTM/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6880XEAH](/tissues/IGVFSM6880XEAH/) 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/IGVFSM6880XEAH/"
}
]
},
"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": "2025-03-05T15:34:41.139055+00:00",
"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/IGVFFI2730WKVI/",
"accession": "IGVFFI2730WKVI",
"aliases": [
"buenrostro-bernstein:SS-LS_8384_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:48.849436+00:00",
"file_format": "fastq",
"file_size": 4125228613,
"href": "/sequence-files/IGVFFI2730WKVI/@@download/IGVFFI2730WKVI.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/ccda7e50-dcb6-4d2a-b6d5-38002eaff983/IGVFFI2730WKVI.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-2254_L5_SS-PKR-604_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5802FITO/",
"accession": "IGVFFI5802FITO",
"aliases": [
"buenrostro-bernstein:SS-LS_8394_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:13.283719+00:00",
"file_format": "fastq",
"file_size": 5783915949,
"href": "/sequence-files/IGVFFI5802FITO/@@download/IGVFFI5802FITO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5948edbd-7bd5-4fbc-a49e-05101c2e4caf/IGVFFI5802FITO.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-2254_L6_SS-PKR-604_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2640BGBT/",
"accession": "IGVFFI2640BGBT",
"aliases": [
"buenrostro-bernstein:SS-LS_8384_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:51.978727+00:00",
"file_format": "fastq",
"file_size": 5739630038,
"href": "/sequence-files/IGVFFI2640BGBT/@@download/IGVFFI2640BGBT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/3e28cfe1-e593-4444-9343-168d747dc49d/IGVFFI2640BGBT.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-2254_L5_SS-PKR-604_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4277WVPZ/",
"accession": "IGVFFI4277WVPZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8394_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:11.108883+00:00",
"file_format": "fastq",
"file_size": 4153971821,
"href": "/sequence-files/IGVFFI4277WVPZ/@@download/IGVFFI4277WVPZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/03ccf52b-cdca-4b42-8946-1aa93dc951fe/IGVFFI4277WVPZ.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-2254_L6_SS-PKR-604_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7596WPAY/",
"accession": "IGVFFI7596WPAY",
"aliases": [
"buenrostro-bernstein:SS-LS_8374_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:30.664021+00:00",
"file_format": "fastq",
"file_size": 5755636869,
"href": "/sequence-files/IGVFFI7596WPAY/@@download/IGVFFI7596WPAY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5de8674b-1be3-47c2-aeae-52aa5c0d9434/IGVFFI7596WPAY.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-2254_L4_SS-PKR-604_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4895WPSA/",
"accession": "IGVFFI4895WPSA",
"aliases": [
"buenrostro-bernstein:SS-LS_8374_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:28.733554+00:00",
"file_format": "fastq",
"file_size": 4108936552,
"href": "/sequence-files/IGVFFI4895WPSA/@@download/IGVFFI4895WPSA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/2a80358a-5060-4c1c-b113-ca6cdb1ae7f6/IGVFFI4895WPSA.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-2254_L4_SS-PKR-604_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8647XLGU/",
"accession": "IGVFFI8647XLGU",
"aliases": [
"buenrostro-bernstein:SS-LS_8394_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:39.175921+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI8647XLGU/@@download/IGVFFI8647XLGU.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/0716029c-7526-40d1-b798-1ca70dde201b/IGVFFI8647XLGU.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8394_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4990ZQDX/",
"accession": "IGVFFI4990ZQDX",
"aliases": [
"buenrostro-bernstein:SS-LS_8384_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:27.985754+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI4990ZQDX/@@download/IGVFFI4990ZQDX.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/d1f447f1-891c-46b4-ae24-1d04d314d060/IGVFFI4990ZQDX.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8384_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1764CSGQ/",
"accession": "IGVFFI1764CSGQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8374_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:17.816175+00:00",
"file_format": "yaml",
"file_size": 1249,
"href": "/configuration-files/IGVFFI1764CSGQ/@@download/IGVFFI1764CSGQ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/065df37f-e6ce-4db4-8714-ddbc63365d1d/IGVFFI1764CSGQ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8374_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8090XCBB/"
],
"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/IGVFDS8262FLXH/",
"accession": "IGVFDS8262FLXH",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:05.285852+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6880XEAH/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6880XEAH",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 604"
],
"cellular_sub_pool": "SS-PKR 604",
"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 604)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:59:28.733554+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "cd1fc63a-3b84-4329-8eb6-9133aa713131"
}