{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2449MQOK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2449MQOK",
"aliases": [
"buenrostro-bernstein:scRNA Lib 844"
],
"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 [IGVFDS2449MQOK](/measurement-sets/IGVFDS2449MQOK/) 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/IGVFDS2449MQOK/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2449MQOK](/measurement-sets/IGVFDS2449MQOK/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2449MQOK/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2449MQOK](/measurement-sets/IGVFDS2449MQOK/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2449MQOK/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM1668LOKY](/tissues/IGVFSM1668LOKY/) 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/IGVFSM1668LOKY/"
},
{
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS2449MQOK](/measurement-sets/IGVFDS2449MQOK/) 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/IGVFDS2449MQOK/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1668LOKY](/tissues/IGVFSM1668LOKY/) 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/IGVFSM1668LOKY/"
}
]
},
"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": "2025-03-05T15:34:08.786510+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/IGVFFI5922XZRC/",
"accession": "IGVFFI5922XZRC",
"aliases": [
"buenrostro-bernstein:SS-LS_8425_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:58.147671+00:00",
"file_format": "fastq",
"file_size": 3816705295,
"href": "/sequence-files/IGVFFI5922XZRC/@@download/IGVFFI5922XZRC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9d86ecfc-1e9c-48c7-bcdb-a1128cf748e8/IGVFFI5922XZRC.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-2245_L3_SS-PKR-605_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7429WSXX/",
"accession": "IGVFFI7429WSXX",
"aliases": [
"buenrostro-bernstein:SS-LS_8425_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:00.716158+00:00",
"file_format": "fastq",
"file_size": 6520646628,
"href": "/sequence-files/IGVFFI7429WSXX/@@download/IGVFFI7429WSXX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/368abb75-6109-4faa-8370-8b6e8d30cfe7/IGVFFI7429WSXX.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-2245_L3_SS-PKR-605_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4790OIUA/",
"accession": "IGVFFI4790OIUA",
"aliases": [
"buenrostro-bernstein:SS-LS_8405_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:19.769031+00:00",
"file_format": "fastq",
"file_size": 6548822441,
"href": "/sequence-files/IGVFFI4790OIUA/@@download/IGVFFI4790OIUA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6f8fd421-e090-48ae-8a14-01d6027077c5/IGVFFI4790OIUA.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-2245_L1_SS-PKR-605_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7885SICC/",
"accession": "IGVFFI7885SICC",
"aliases": [
"buenrostro-bernstein:SS-LS_8415_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:36.439294+00:00",
"file_format": "fastq",
"file_size": 3815163015,
"href": "/sequence-files/IGVFFI7885SICC/@@download/IGVFFI7885SICC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9c55e7ef-7da1-4d07-8b8a-4d53cf2316f6/IGVFFI7885SICC.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-2245_L2_SS-PKR-605_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4338OVYC/",
"accession": "IGVFFI4338OVYC",
"aliases": [
"buenrostro-bernstein:SS-LS_8405_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:17.922324+00:00",
"file_format": "fastq",
"file_size": 3830114346,
"href": "/sequence-files/IGVFFI4338OVYC/@@download/IGVFFI4338OVYC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/1b2e734e-748e-41ab-b347-51e5643c22a6/IGVFFI4338OVYC.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-2245_L1_SS-PKR-605_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3595CRAV/",
"accession": "IGVFFI3595CRAV",
"aliases": [
"buenrostro-bernstein:SS-LS_8415_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:38.410007+00:00",
"file_format": "fastq",
"file_size": 6508109214,
"href": "/sequence-files/IGVFFI3595CRAV/@@download/IGVFFI3595CRAV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/ce53eb50-5966-44b2-91ee-d9c2b905c108/IGVFFI3595CRAV.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-2245_L2_SS-PKR-605_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8665QPKQ/",
"accession": "IGVFFI8665QPKQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8415_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:38.987600+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI8665QPKQ/@@download/IGVFFI8665QPKQ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/11f4358d-340b-4faa-bb2a-b87a1aaebc6d/IGVFFI8665QPKQ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8415_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8080HBHK/",
"accession": "IGVFFI8080HBHK",
"aliases": [
"buenrostro-bernstein:SS-LS_8405_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:27.958545+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI8080HBHK/@@download/IGVFFI8080HBHK.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/cd606e7f-a863-40fd-a98e-82599bbbb3fb/IGVFFI8080HBHK.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8405_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4236DTAC/",
"accession": "IGVFFI4236DTAC",
"aliases": [
"buenrostro-bernstein:SS-LS_8425_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:48.786328+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI4236DTAC/@@download/IGVFFI4236DTAC.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/f55dc3d2-f001-4a24-836c-874332d1c5e7/IGVFFI4236DTAC.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8425_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4479WEBI/"
],
"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/IGVFDS1036WPFQ/",
"accession": "IGVFDS1036WPFQ",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:32.012355+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1668LOKY/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1668LOKY",
"aliases": [
"buenrostro-bernstein:BioSam 5155_SS-PKR 605"
],
"cellular_sub_pool": "SS-PKR 605",
"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 605)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:55:17.922324+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "88fb45bd-c083-4a53-8c26-f9c5c4406ba1"
}