{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2423IQUI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2423IQUI",
"aliases": [
"buenrostro-bernstein:scRNA Lib 807"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2423IQUI](/measurement-sets/IGVFDS2423IQUI/) 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/IGVFDS2423IQUI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2423IQUI](/measurement-sets/IGVFDS2423IQUI/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2423IQUI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2423IQUI](/measurement-sets/IGVFDS2423IQUI/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2423IQUI/"
},
{
"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 [IGVFSM4295RKOR](/tissues/IGVFSM4295RKOR/) 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/IGVFSM4295RKOR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS2423IQUI](/measurement-sets/IGVFDS2423IQUI/) 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/IGVFDS2423IQUI/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM4295RKOR](/tissues/IGVFSM4295RKOR/) 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/IGVFSM4295RKOR/"
}
]
},
"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": "2025-03-05T15:33:50.209882+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/IGVFFI8870DBBG/",
"accession": "IGVFFI8870DBBG",
"aliases": [
"buenrostro-bernstein:SS-LS_8360_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:53:49.625309+00:00",
"file_format": "fastq",
"file_size": 1319706615,
"href": "/sequence-files/IGVFFI8870DBBG/@@download/IGVFFI8870DBBG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f33185e7-c7c5-4bca-95ab-826d111580ab/IGVFFI8870DBBG.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-2214_L7_SS-PKR-533_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5614NFUR/",
"accession": "IGVFFI5614NFUR",
"aliases": [
"buenrostro-bernstein:SS-LS_8304_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:43.622088+00:00",
"file_format": "fastq",
"file_size": 5759586021,
"href": "/sequence-files/IGVFFI5614NFUR/@@download/IGVFFI5614NFUR.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9b7afdc9-9bad-44fd-8b4a-ba1e04b826cb/IGVFFI5614NFUR.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-2174_L6_SS-PKR-533_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3840FILQ/",
"accession": "IGVFFI3840FILQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8304_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:45.648879+00:00",
"file_format": "fastq",
"file_size": 10635966728,
"href": "/sequence-files/IGVFFI3840FILQ/@@download/IGVFFI3840FILQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/ef29625e-f98f-47a1-b5d5-0dae6ac9f2e1/IGVFFI3840FILQ.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-2174_L6_SS-PKR-533_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5610AHGI/",
"accession": "IGVFFI5610AHGI",
"aliases": [
"buenrostro-bernstein:SS-LS_8360_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:53:51.192094+00:00",
"file_format": "fastq",
"file_size": 2236052604,
"href": "/sequence-files/IGVFFI5610AHGI/@@download/IGVFFI5610AHGI.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6cba32b2-3cc1-4733-8605-09c2725ca469/IGVFFI5610AHGI.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-2214_L7_SS-PKR-533_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8812JDSN/",
"accession": "IGVFFI8812JDSN",
"aliases": [
"buenrostro-bernstein:SS-LS_8304_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:56:54.174899+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI8812JDSN/@@download/IGVFFI8812JDSN.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/da5497b3-86af-4bd9-aed9-831663704cf8/IGVFFI8812JDSN.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8304_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2562BNWT/",
"accession": "IGVFFI2562BNWT",
"aliases": [
"buenrostro-bernstein:SS-LS_8360_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:11.048302+00:00",
"file_format": "yaml",
"file_size": 1285,
"href": "/configuration-files/IGVFFI2562BNWT/@@download/IGVFFI2562BNWT.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/da62187f-b7a0-47da-a10d-435c46c73f6b/IGVFFI2562BNWT.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8360_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9179TXUS/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI6680XCDT/",
"/tabular-files/IGVFFI2668ZFEB/"
],
"onlist_method": "multi",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS6783BLZB/",
"accession": "IGVFDS6783BLZB",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:47.346751+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM4295RKOR/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4295RKOR",
"aliases": [
"buenrostro-bernstein:BioSam 5152_SS-PKR 533"
],
"cellular_sub_pool": "SS-PKR 533",
"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 533)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:52:43.622088+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "e0644aaf-05ca-48f7-9221-ae5824a2a33c"
}