{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9040WICU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9040WICU",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1784"
],
"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 [IGVFDS9040WICU](/measurement-sets/IGVFDS9040WICU/) 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/IGVFDS9040WICU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9040WICU](/measurement-sets/IGVFDS9040WICU/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9040WICU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9040WICU](/measurement-sets/IGVFDS9040WICU/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9040WICU/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM9869JVFX](/tissues/IGVFSM9869JVFX/) 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/IGVFSM9869JVFX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9040WICU](/measurement-sets/IGVFDS9040WICU/) 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/IGVFDS9040WICU/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9869JVFX](/tissues/IGVFSM9869JVFX/) 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/IGVFSM9869JVFX/"
}
]
},
"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": "2025-03-05T15:34:03.853166+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3508PMXX/",
"accession": "IGVFDO3508PMXX",
"aliases": [
"ali-mortazavi:768_B6J_10F",
"buenrostro-bernstein:Donor 2078"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6964MSYU/",
"accession": "IGVFFI6964MSYU",
"aliases": [
"buenrostro-bernstein:SS-LS_8377_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:17.735696+00:00",
"file_format": "fastq",
"file_size": 3137765926,
"href": "/sequence-files/IGVFFI6964MSYU/@@download/IGVFFI6964MSYU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/95172a5d-73c0-4a02-ba0c-6fbc72dccd02/IGVFFI6964MSYU.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-2257_L4_SS-PKR-607_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0208AMKP/",
"accession": "IGVFFI0208AMKP",
"aliases": [
"buenrostro-bernstein:SS-LS_8377_R2"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:19.729325+00:00",
"file_format": "fastq",
"file_size": 4343275107,
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"s3_uri": "s3://igvf-files/2025/03/05/a2f2cc23-24a0-458f-b51c-c26700bf7c18/IGVFFI0208AMKP.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-2257_L4_SS-PKR-607_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7747SCLS/",
"accession": "IGVFFI7747SCLS",
"aliases": [
"buenrostro-bernstein:SS-LS_8387_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:37.659984+00:00",
"file_format": "fastq",
"file_size": 3123385054,
"href": "/sequence-files/IGVFFI7747SCLS/@@download/IGVFFI7747SCLS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/60b3d3b9-8266-4f9d-aa5d-8baeb1c62e67/IGVFFI7747SCLS.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-2257_L5_SS-PKR-607_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3687YIBD/",
"accession": "IGVFFI3687YIBD",
"aliases": [
"buenrostro-bernstein:SS-LS_8397_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:03.711737+00:00",
"file_format": "fastq",
"file_size": 4293956587,
"href": "/sequence-files/IGVFFI3687YIBD/@@download/IGVFFI3687YIBD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/71a862ab-2f57-4d60-bc70-01922b00f16d/IGVFFI3687YIBD.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-2257_L6_SS-PKR-607_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6204YTKS/",
"accession": "IGVFFI6204YTKS",
"aliases": [
"buenrostro-bernstein:SS-LS_8387_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:40.902187+00:00",
"file_format": "fastq",
"file_size": 4295736594,
"href": "/sequence-files/IGVFFI6204YTKS/@@download/IGVFFI6204YTKS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/74d1cd92-36bd-42e5-8ca6-b067d54a6408/IGVFFI6204YTKS.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-2257_L5_SS-PKR-607_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6734TCOY/",
"accession": "IGVFFI6734TCOY",
"aliases": [
"buenrostro-bernstein:SS-LS_8397_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:00.351739+00:00",
"file_format": "fastq",
"file_size": 3121169615,
"href": "/sequence-files/IGVFFI6734TCOY/@@download/IGVFFI6734TCOY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5883e141-b02b-411d-bfc5-f1c329c33357/IGVFFI6734TCOY.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2257_L6_SS-PKR-607_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2343DHJQ/",
"accession": "IGVFFI2343DHJQ",
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"buenrostro-bernstein:SS-LS_8397_seqspec"
],
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"creation_timestamp": "2025-03-07T20:00:27.590247+00:00",
"file_format": "yaml",
"file_size": 1249,
"href": "/configuration-files/IGVFFI2343DHJQ/@@download/IGVFFI2343DHJQ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/b4bb8f2f-a80a-4343-b044-30aa99ba3fce/IGVFFI2343DHJQ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8397_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5767TNGL/",
"accession": "IGVFFI5767TNGL",
"aliases": [
"buenrostro-bernstein:SS-LS_8387_seqspec"
],
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"creation_timestamp": "2025-03-07T20:00:16.836074+00:00",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8496ATXD/",
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"buenrostro-bernstein:SS-LS_8377_seqspec"
],
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"creation_timestamp": "2025-03-07T20:00:04.561643+00:00",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8377_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2842HNUG/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
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"/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/IGVFDS5127PEXX/",
"accession": "IGVFDS5127PEXX",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:39.274379+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9869JVFX/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9869JVFX",
"aliases": [
"buenrostro-bernstein:BioSam 5155_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 C57BL/6J (female) 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/",
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},
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"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "ddc3fe2f-01e3-43d0-bb9c-39e80f9c55c6"
}