{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5417MWZF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5417MWZF",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1555"
],
"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 [IGVFDS5417MWZF](/measurement-sets/IGVFDS5417MWZF/) 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/IGVFDS5417MWZF/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5417MWZF](/measurement-sets/IGVFDS5417MWZF/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5417MWZF/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5417MWZF](/measurement-sets/IGVFDS5417MWZF/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5417MWZF/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM9059OMXR](/tissues/IGVFSM9059OMXR/) 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/IGVFSM9059OMXR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5417MWZF](/measurement-sets/IGVFDS5417MWZF/) 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/IGVFDS5417MWZF/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9059OMXR](/tissues/IGVFSM9059OMXR/) 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/IGVFSM9059OMXR/"
}
]
},
"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": "2025-03-05T15:33:43.642173+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/IGVFFI5838QXAW/",
"accession": "IGVFFI5838QXAW",
"aliases": [
"buenrostro-bernstein:SS-LS_8342_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:53:20.397106+00:00",
"file_format": "fastq",
"file_size": 2755727642,
"href": "/sequence-files/IGVFFI5838QXAW/@@download/IGVFFI5838QXAW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/8ec45552-8d05-42d0-bc20-76e616852a07/IGVFFI5838QXAW.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-2228_L8_SS-PKR-532_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6344JGXG/",
"accession": "IGVFFI6344JGXG",
"aliases": [
"buenrostro-bernstein:SS-LS_8342_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:53:18.452833+00:00",
"file_format": "fastq",
"file_size": 1962895174,
"href": "/sequence-files/IGVFFI6344JGXG/@@download/IGVFFI6344JGXG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/00e5e15e-8e15-4732-92e0-a64cc18e1f12/IGVFFI6344JGXG.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-2228_L8_SS-PKR-532_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0279UFOQ/",
"accession": "IGVFFI0279UFOQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8278_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:25.357666+00:00",
"file_format": "fastq",
"file_size": 2983196992,
"href": "/sequence-files/IGVFFI0279UFOQ/@@download/IGVFFI0279UFOQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d519d41b-1caf-41a0-9973-098dff5c81ee/IGVFFI0279UFOQ.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-2156_L2_SS-PKR-532_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2096LEPL/",
"accession": "IGVFFI2096LEPL",
"aliases": [
"buenrostro-bernstein:SS-LS_8278_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:27.152853+00:00",
"file_format": "fastq",
"file_size": 4226954583,
"href": "/sequence-files/IGVFFI2096LEPL/@@download/IGVFFI2096LEPL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/56559497-8db3-4619-8e04-ae226f7c66ba/IGVFFI2096LEPL.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-2156_L2_SS-PKR-532_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1884VVLA/",
"accession": "IGVFFI1884VVLA",
"aliases": [
"buenrostro-bernstein:SS-LS_8342_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:42.405551+00:00",
"file_format": "yaml",
"file_size": 1252,
"href": "/configuration-files/IGVFFI1884VVLA/@@download/IGVFFI1884VVLA.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/cee3ca19-d599-4d2c-a9db-ef3aae094402/IGVFFI1884VVLA.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8342_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8044WCRU/",
"accession": "IGVFFI8044WCRU",
"aliases": [
"buenrostro-bernstein:SS-LS_8278_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:26.980260+00:00",
"file_format": "yaml",
"file_size": 1252,
"href": "/configuration-files/IGVFFI8044WCRU/@@download/IGVFFI8044WCRU.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/177528db-2d4f-445d-a883-ebf73e5adceb/IGVFFI8044WCRU.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8278_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9994WODZ/"
],
"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/IGVFDS3140HFWZ/",
"accession": "IGVFDS3140HFWZ",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:03.591335+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9059OMXR/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9059OMXR",
"aliases": [
"buenrostro-bernstein:BioSam 5152_SS-PKR 532"
],
"cellular_sub_pool": "SS-PKR 532",
"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 532)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:52:25.357666+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "9a4535af-06f6-41bc-8e06-21839c2823b2"
}