{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5192VPKQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5192VPKQ",
"aliases": [
"bradley-bernstein:scRNA Lib 72",
"buenrostro-bernstein:scRNA Lib 72"
],
"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 [IGVFDS5192VPKQ](/measurement-sets/IGVFDS5192VPKQ/) 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/IGVFDS5192VPKQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5192VPKQ](/measurement-sets/IGVFDS5192VPKQ/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5192VPKQ/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM3932SXVT](/tissues/IGVFSM3932SXVT/) 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/IGVFSM3932SXVT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5192VPKQ](/measurement-sets/IGVFDS5192VPKQ/) 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/IGVFDS5192VPKQ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM3932SXVT](/tissues/IGVFSM3932SXVT/) 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/IGVFSM3932SXVT/"
}
]
},
"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": "2023-08-28T20:29:07.006690+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO1318PLKS/",
"accession": "IGVFDO1318PLKS",
"aliases": [
"bradley-bernstein:Donor 1503",
"buenrostro-bernstein:Donor 1503"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6975THFK/",
"accession": "IGVFFI6975THFK",
"aliases": [
"bradley-bernstein:SS-LS_1981_R1",
"bradley-bernstein:SS-LS_63_R1",
"buenrostro-bernstein:SS-LS_1981_R1",
"buenrostro-bernstein:SS-LS_63_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:47.240502+00:00",
"file_format": "fastq",
"file_size": 563683742,
"href": "/sequence-files/IGVFFI6975THFK/@@download/IGVFFI6975THFK.fastq.gz",
"md5sum": "11bf9fb976306db4105db43a7230b6f2",
"s3_uri": "s3://igvf-files/2023/09/05/27f9fd2c-05e0-4606-925e-1b6ca6d20b51/IGVFFI6975THFK.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-134_L1_SS-PKR-129_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0992VCWH/",
"accession": "IGVFFI0992VCWH",
"aliases": [
"bradley-bernstein:SS-LS_1981_R2",
"bradley-bernstein:SS-LS_63_R2",
"buenrostro-bernstein:SS-LS_1981_R2",
"buenrostro-bernstein:SS-LS_63_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:48.113933+00:00",
"file_format": "fastq",
"file_size": 1021052928,
"href": "/sequence-files/IGVFFI0992VCWH/@@download/IGVFFI0992VCWH.fastq.gz",
"md5sum": "a716bbeb8c4b7b523790a79392195145",
"s3_uri": "s3://igvf-files/2023/09/05/a2015c09-c096-4242-9618-0a10ae551f5a/IGVFFI0992VCWH.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-134_L1_SS-PKR-129_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1478VZJX/",
"accession": "IGVFFI1478VZJX",
"aliases": [
"bradley-bernstein:SS-LS_2009_R2",
"bradley-bernstein:SS-LS_247_R2",
"buenrostro-bernstein:SS-LS_2009_R2",
"buenrostro-bernstein:SS-LS_247_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:59.240291+00:00",
"file_format": "fastq",
"file_size": 1022969655,
"href": "/sequence-files/IGVFFI1478VZJX/@@download/IGVFFI1478VZJX.fastq.gz",
"md5sum": "547fc904ac559c86e6fdaf9c7583953c",
"s3_uri": "s3://igvf-files/2023/09/05/05b1614f-4f93-4a7a-a3e6-888e36a127d6/IGVFFI1478VZJX.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-134_L2_SS-PKR-129_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4562ZCKO/",
"accession": "IGVFFI4562ZCKO",
"aliases": [
"bradley-bernstein:SS-LS_2009_R1",
"bradley-bernstein:SS-LS_247_R1",
"buenrostro-bernstein:SS-LS_2009_R1",
"buenrostro-bernstein:SS-LS_247_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:58.347692+00:00",
"file_format": "fastq",
"file_size": 563853112,
"href": "/sequence-files/IGVFFI4562ZCKO/@@download/IGVFFI4562ZCKO.fastq.gz",
"md5sum": "86a68d3954966763979091de2dfe1a0d",
"s3_uri": "s3://igvf-files/2023/09/05/83a87228-3520-4396-ad2c-ed6bec67e9e3/IGVFFI4562ZCKO.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-134_L2_SS-PKR-129_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0896MCPD/",
"accession": "IGVFFI0896MCPD",
"aliases": [
"buenrostro-bernstein:SS-LS_2009_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:42.012270+00:00",
"file_format": "yaml",
"file_size": 1231,
"href": "/configuration-files/IGVFFI0896MCPD/@@download/IGVFFI0896MCPD.yaml.gz",
"md5sum": "1daeb8a73daeb7b55894f11d4ec76b01",
"s3_uri": "s3://igvf-files/2024/09/17/c70a4b86-77bb-4b8c-9818-e19be0b96e3e/IGVFFI0896MCPD.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2009_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7946BPBO/",
"accession": "IGVFFI7946BPBO",
"aliases": [
"buenrostro-bernstein:SS-LS_1981_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:48.678849+00:00",
"file_format": "yaml",
"file_size": 1231,
"href": "/configuration-files/IGVFFI7946BPBO/@@download/IGVFFI7946BPBO.yaml.gz",
"md5sum": "06fbfb24d0a6631fa22c754838610e04",
"s3_uri": "s3://igvf-files/2024/09/17/225ac665-61bb-447b-a066-c203e99b0a70/IGVFFI7946BPBO.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_1981_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8415FVDT/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 6,
"notes": "Preferred_assay_titles enum SHARE-Seq has been renamed to be SHARE-seq.",
"onlist_files": [
"/tabular-files/IGVFFI0400MBIM/"
],
"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/IGVFDS0020LQRY/",
"accession": "IGVFDS0020LQRY",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4911ZDCJ/",
"accession": "IGVFDS4911ZDCJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8535JZRF/",
"accession": "IGVFDS8535JZRF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3638UVNV/",
"accession": "IGVFDS3638UVNV",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8078FJZR/",
"accession": "IGVFDS8078FJZR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:33.498351+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM3932SXVT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3932SXVT",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 129",
"buenrostro-bernstein:BioSam 4561_SS-PKR 129"
],
"cellular_sub_pool": "SS-PKR 129",
"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 (female) brain tissue (cellular sub pool: SS-PKR 129)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-09-05T19:27:47.240502+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "e3916a40-5221-46dc-9ede-811ddcecaafb"
}