{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6289YQBN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6289YQBN",
"aliases": [
"buenrostro-bernstein:scRNA Lib 601"
],
"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 [IGVFSM4321WQTD](/tissues/IGVFSM4321WQTD/) 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/IGVFSM4321WQTD/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6289YQBN](/measurement-sets/IGVFDS6289YQBN/) 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/IGVFDS6289YQBN/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6289YQBN](/measurement-sets/IGVFDS6289YQBN/) has in progress subobject tabular file [IGVFFI9034HUWG](/tabular-files/IGVFFI9034HUWG/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6289YQBN/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6289YQBN](/measurement-sets/IGVFDS6289YQBN/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6289YQBN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6289YQBN](/measurement-sets/IGVFDS6289YQBN/) 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/IGVFDS6289YQBN/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM4321WQTD](/tissues/IGVFSM4321WQTD/) 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/IGVFSM4321WQTD/"
}
]
},
"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": "2025-03-09T15:52:15.351761+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO9446AKYF/",
"accession": "IGVFDO9446AKYF",
"aliases": [
"buenrostro-bernstein:Donor 2047"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI0846GWZX/",
"accession": "IGVFFI0846GWZX",
"aliases": [
"buenrostro-bernstein:SS-LS_3818_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:01:13.489607+00:00",
"file_format": "fastq",
"file_size": 1822004842,
"href": "/sequence-files/IGVFFI0846GWZX/@@download/IGVFFI0846GWZX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/fe67e389-ce4c-4617-a7a2-e6ed50e6d315/IGVFFI0846GWZX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1539_L1_SS-PKR-436_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4188BVSG/",
"accession": "IGVFFI4188BVSG",
"aliases": [
"buenrostro-bernstein:SS-LS_3818_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:01:11.942484+00:00",
"file_format": "fastq",
"file_size": 1116320736,
"href": "/sequence-files/IGVFFI4188BVSG/@@download/IGVFFI4188BVSG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/8e736ed6-fd0a-444a-95d0-823985be934c/IGVFFI4188BVSG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1539_L1_SS-PKR-436_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8647WTOX/",
"accession": "IGVFFI8647WTOX",
"aliases": [
"buenrostro-bernstein:SS-LS_3842_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:00:56.195028+00:00",
"file_format": "fastq",
"file_size": 1874736111,
"href": "/sequence-files/IGVFFI8647WTOX/@@download/IGVFFI8647WTOX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/bc1a6c9f-1756-4264-a0ba-a4bdc49fecac/IGVFFI8647WTOX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1539_L2_SS-PKR-436_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4040KVJA/",
"accession": "IGVFFI4040KVJA",
"aliases": [
"buenrostro-bernstein:SS-LS_3842_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:00:54.861622+00:00",
"file_format": "fastq",
"file_size": 1143755357,
"href": "/sequence-files/IGVFFI4040KVJA/@@download/IGVFFI4040KVJA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/06ce3b1e-1adf-4861-b156-1f22a6f51f9b/IGVFFI4040KVJA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1539_L2_SS-PKR-436_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9557CSJM/",
"accession": "IGVFFI9557CSJM",
"aliases": [
"buenrostro-bernstein:SS-LS_3842_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-13T17:54:24.762103+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI9557CSJM/@@download/IGVFFI9557CSJM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/13/5b4d1da1-b182-4da8-a3a8-67bb769c9170/IGVFFI9557CSJM.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_3842_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4735KTCJ/",
"accession": "IGVFFI4735KTCJ",
"aliases": [
"buenrostro-bernstein:SS-LS_3818_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-13T17:54:34.206214+00:00",
"file_format": "yaml",
"file_size": 1290,
"href": "/configuration-files/IGVFFI4735KTCJ/@@download/IGVFFI4735KTCJ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/13/55a87c2a-0f1a-4ba7-bbab-a567f66911c8/IGVFFI4735KTCJ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_3818_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6753PKAH/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 5,
"onlist_files": [
"/tabular-files/IGVFFI9034HUWG/",
"/tabular-files/IGVFFI0400MBIM/"
],
"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/IGVFDS4752BWME/",
"accession": "IGVFDS4752BWME",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5083GBBF/",
"accession": "IGVFDS5083GBBF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7571FXYP/",
"accession": "IGVFDS7571FXYP",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5177YHMM/",
"accession": "IGVFDS5177YHMM",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:59.925250+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM4321WQTD/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4321WQTD",
"aliases": [
"buenrostro-bernstein:BioSam 4965_SS-PKR 436"
],
"cellular_sub_pool": "SS-PKR 436",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000955/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "brain",
"term_name": "brain"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 436)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-09T16:00:54.861622+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "df083373-b4fe-4777-b958-5fbeb7fcf421"
}