{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0313KPRX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0313KPRX",
"aliases": [
"buenrostro-bernstein:scRNA Lib 797"
],
"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": "Tissue [IGVFSM6577YGTD](/tissues/IGVFSM6577YGTD/) 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/IGVFSM6577YGTD/"
},
{
"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 [IGVFDS0313KPRX](/measurement-sets/IGVFDS0313KPRX/) 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/IGVFDS0313KPRX/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0313KPRX](/measurement-sets/IGVFDS0313KPRX/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0313KPRX/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0313KPRX](/measurement-sets/IGVFDS0313KPRX/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0313KPRX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0313KPRX](/measurement-sets/IGVFDS0313KPRX/) 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/IGVFDS0313KPRX/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6577YGTD](/tissues/IGVFSM6577YGTD/) 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/IGVFSM6577YGTD/"
}
]
},
"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": "2025-03-05T15:34:14.084794+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO9355TCPX/",
"accession": "IGVFDO9355TCPX",
"aliases": [
"ali-mortazavi:777_CASTJ_10M",
"buenrostro-bernstein:Donor 2073"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2410UOXP/",
"accession": "IGVFFI2410UOXP",
"aliases": [
"buenrostro-bernstein:SS-LS_7399_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:47.504839+00:00",
"file_format": "fastq",
"file_size": 8363606721,
"href": "/sequence-files/IGVFFI2410UOXP/@@download/IGVFFI2410UOXP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6aa65ef9-647b-49b6-8a09-f3eca75d9452/IGVFFI2410UOXP.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-1958_L8_SS-PKR-502_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4996PJUA/",
"accession": "IGVFFI4996PJUA",
"aliases": [
"buenrostro-bernstein:SS-LS_7393_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:34.658277+00:00",
"file_format": "fastq",
"file_size": 8647021978,
"href": "/sequence-files/IGVFFI4996PJUA/@@download/IGVFFI4996PJUA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/1e5f9b26-39b9-4275-aa82-1c764288ed82/IGVFFI4996PJUA.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-1958_L7_SS-PKR-502_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7092LWDD/",
"accession": "IGVFFI7092LWDD",
"aliases": [
"buenrostro-bernstein:SS-LS_7399_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:49.522212+00:00",
"file_format": "fastq",
"file_size": 14640009567,
"href": "/sequence-files/IGVFFI7092LWDD/@@download/IGVFFI7092LWDD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/731c0ce7-e308-47eb-8c2c-257839dea3d7/IGVFFI7092LWDD.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-1958_L8_SS-PKR-502_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6905BQKT/",
"accession": "IGVFFI6905BQKT",
"aliases": [
"buenrostro-bernstein:SS-LS_7393_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:36.406566+00:00",
"file_format": "fastq",
"file_size": 15413317853,
"href": "/sequence-files/IGVFFI6905BQKT/@@download/IGVFFI6905BQKT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9aceb936-d13f-4b75-a25e-286b4c7895af/IGVFFI6905BQKT.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-1958_L7_SS-PKR-502_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5596OJWV/",
"accession": "IGVFFI5596OJWV",
"aliases": [
"buenrostro-bernstein:SS-LS_7399_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:59.372862+00:00",
"file_format": "yaml",
"file_size": 1292,
"href": "/configuration-files/IGVFFI5596OJWV/@@download/IGVFFI5596OJWV.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/f78e1697-ac88-4dc9-8a4e-ce7f99afffa6/IGVFFI5596OJWV.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7399_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0457JTEV/",
"accession": "IGVFFI0457JTEV",
"aliases": [
"buenrostro-bernstein:SS-LS_7393_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:52.810283+00:00",
"file_format": "yaml",
"file_size": 1289,
"href": "/configuration-files/IGVFFI0457JTEV/@@download/IGVFFI0457JTEV.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/56d252e6-dd75-4fa2-895b-af5c75e534d1/IGVFFI0457JTEV.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7393_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1123ICRW/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI3897QKNI/",
"/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/IGVFDS7549ZYDK/",
"accession": "IGVFDS7549ZYDK",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:17:54.271187+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6577YGTD/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6577YGTD",
"aliases": [
"buenrostro-bernstein:BioSam 5150_SS-PKR 502"
],
"cellular_sub_pool": "SS-PKR 502",
"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 CASTJ (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 502)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:56:34.658277+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "bf027eb7-a8a1-4aa3-b134-0b0bd5f12414"
}