{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0421VWRP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0421VWRP",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1775"
],
"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 [IGVFSM9638OVAV](/tissues/IGVFSM9638OVAV/) 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/IGVFSM9638OVAV/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0421VWRP](/measurement-sets/IGVFDS0421VWRP/) 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/IGVFDS0421VWRP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0421VWRP](/measurement-sets/IGVFDS0421VWRP/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0421VWRP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0421VWRP](/measurement-sets/IGVFDS0421VWRP/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0421VWRP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0421VWRP](/measurement-sets/IGVFDS0421VWRP/) 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/IGVFDS0421VWRP/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9638OVAV](/tissues/IGVFSM9638OVAV/) 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/IGVFSM9638OVAV/"
}
]
},
"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": "2025-03-05T15:34:38.948561+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/IGVFFI5966LUIA/",
"accession": "IGVFFI5966LUIA",
"aliases": [
"buenrostro-bernstein:SS-LS_8370_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:21.974179+00:00",
"file_format": "fastq",
"file_size": 5047338375,
"href": "/sequence-files/IGVFFI5966LUIA/@@download/IGVFFI5966LUIA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/63b6a13d-6dd9-4875-b39a-85afa543970a/IGVFFI5966LUIA.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-2250_L4_SS-PKR-602_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6482SOPN/",
"accession": "IGVFFI6482SOPN",
"aliases": [
"buenrostro-bernstein:SS-LS_8380_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:41.223101+00:00",
"file_format": "fastq",
"file_size": 3605242573,
"href": "/sequence-files/IGVFFI6482SOPN/@@download/IGVFFI6482SOPN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/185ca88c-4471-47da-8e8b-e33aabfa718a/IGVFFI6482SOPN.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-2250_L5_SS-PKR-602_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6403PCEX/",
"accession": "IGVFFI6403PCEX",
"aliases": [
"buenrostro-bernstein:SS-LS_8370_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:19.899921+00:00",
"file_format": "fastq",
"file_size": 3606154176,
"href": "/sequence-files/IGVFFI6403PCEX/@@download/IGVFFI6403PCEX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/de43f5d3-d812-43ac-ad77-d0bbb689ec56/IGVFFI6403PCEX.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-2250_L4_SS-PKR-602_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9869UBGQ/",
"accession": "IGVFFI9869UBGQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8380_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:42.927799+00:00",
"file_format": "fastq",
"file_size": 5010383968,
"href": "/sequence-files/IGVFFI9869UBGQ/@@download/IGVFFI9869UBGQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/c41655fa-e472-4d0c-9d50-8b5d8f9112b1/IGVFFI9869UBGQ.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-2250_L5_SS-PKR-602_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7536GPYC/",
"accession": "IGVFFI7536GPYC",
"aliases": [
"buenrostro-bernstein:SS-LS_8390_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:02.707370+00:00",
"file_format": "fastq",
"file_size": 3606304431,
"href": "/sequence-files/IGVFFI7536GPYC/@@download/IGVFFI7536GPYC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9c6a2550-47df-4b7e-9d31-b72eddfa10bc/IGVFFI7536GPYC.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-2250_L6_SS-PKR-602_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9219JXDB/",
"accession": "IGVFFI9219JXDB",
"aliases": [
"buenrostro-bernstein:SS-LS_8390_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:04.872571+00:00",
"file_format": "fastq",
"file_size": 5013236051,
"href": "/sequence-files/IGVFFI9219JXDB/@@download/IGVFFI9219JXDB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/45cc387d-ef1d-4325-8ba7-932a509f0d2d/IGVFFI9219JXDB.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-2250_L6_SS-PKR-602_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9328LLDG/",
"accession": "IGVFFI9328LLDG",
"aliases": [
"buenrostro-bernstein:SS-LS_8380_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:23.747825+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI9328LLDG/@@download/IGVFFI9328LLDG.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/4d8729e3-8162-437c-bb3b-28935a283eb7/IGVFFI9328LLDG.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8380_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3927KZUT/",
"accession": "IGVFFI3927KZUT",
"aliases": [
"buenrostro-bernstein:SS-LS_8390_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:35.393721+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI3927KZUT/@@download/IGVFFI3927KZUT.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/a665cd98-25b7-4c64-9d4d-4d43dd6dcbeb/IGVFFI3927KZUT.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8390_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4242QLEQ/",
"accession": "IGVFFI4242QLEQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8370_seqspec"
],
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"creation_timestamp": "2025-03-07T20:01:14.091686+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI4242QLEQ/@@download/IGVFFI4242QLEQ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/753123be-cdc0-4832-b88f-1c8dd73f84b9/IGVFFI4242QLEQ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8370_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1883ZXNX/"
],
"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/IGVFDS1530NDJN/",
"accession": "IGVFDS1530NDJN",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:14.692333+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9638OVAV/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9638OVAV",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 602"
],
"cellular_sub_pool": "SS-PKR 602",
"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 602)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:59:19.899921+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "b42009bd-c550-4b4d-bb3b-aa05efb20cef"
}