{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8078FJZR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8078FJZR",
"aliases": [
"bradley-bernstein:scRNA Lib 71",
"buenrostro-bernstein:scRNA Lib 71"
],
"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 [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/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8078FJZR](/measurement-sets/IGVFDS8078FJZR/) 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/IGVFDS8078FJZR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8078FJZR](/measurement-sets/IGVFDS8078FJZR/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8078FJZR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8078FJZR](/measurement-sets/IGVFDS8078FJZR/) 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/IGVFDS8078FJZR/"
}
],
"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": "2023-08-28T20:29:07.529055+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/IGVFFI3630LZMZ/",
"accession": "IGVFFI3630LZMZ",
"aliases": [
"bradley-bernstein:SS-LS_1980_R1",
"bradley-bernstein:SS-LS_64_R1",
"buenrostro-bernstein:SS-LS_1980_R1",
"buenrostro-bernstein:SS-LS_64_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:49.088778+00:00",
"file_format": "fastq",
"file_size": 356629566,
"href": "/sequence-files/IGVFFI3630LZMZ/@@download/IGVFFI3630LZMZ.fastq.gz",
"md5sum": "4dde0b7e2ef397ab8c948b72def38991",
"s3_uri": "s3://igvf-files/2023/09/05/5a4962f6-b7b2-42b9-8582-d3bba8608c8d/IGVFFI3630LZMZ.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-133_L1_SS-PKR-129_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8093PSPU/",
"accession": "IGVFFI8093PSPU",
"aliases": [
"bradley-bernstein:SS-LS_2008_R1",
"bradley-bernstein:SS-LS_248_R1",
"buenrostro-bernstein:SS-LS_2008_R1",
"buenrostro-bernstein:SS-LS_248_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:28:07.800762+00:00",
"file_format": "fastq",
"file_size": 356803492,
"href": "/sequence-files/IGVFFI8093PSPU/@@download/IGVFFI8093PSPU.fastq.gz",
"md5sum": "5b425c6b70b77882f11112598fc18fdb",
"s3_uri": "s3://igvf-files/2023/09/05/fb7359dc-50de-479b-8596-b94876d2e9e8/IGVFFI8093PSPU.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-133_L2_SS-PKR-129_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0934YZGH/",
"accession": "IGVFFI0934YZGH",
"aliases": [
"bradley-bernstein:SS-LS_1980_R2",
"bradley-bernstein:SS-LS_64_R2",
"buenrostro-bernstein:SS-LS_1980_R2",
"buenrostro-bernstein:SS-LS_64_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:50.008657+00:00",
"file_format": "fastq",
"file_size": 630574429,
"href": "/sequence-files/IGVFFI0934YZGH/@@download/IGVFFI0934YZGH.fastq.gz",
"md5sum": "8973a607e835c9e5b65713b056ad56ab",
"s3_uri": "s3://igvf-files/2023/09/05/567cc650-e02d-4580-91b5-27ad1a034dbe/IGVFFI0934YZGH.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-133_L1_SS-PKR-129_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9300DFWT/",
"accession": "IGVFFI9300DFWT",
"aliases": [
"bradley-bernstein:SS-LS_2008_R2",
"bradley-bernstein:SS-LS_248_R2",
"buenrostro-bernstein:SS-LS_2008_R2",
"buenrostro-bernstein:SS-LS_248_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:28:08.689192+00:00",
"file_format": "fastq",
"file_size": 632083599,
"href": "/sequence-files/IGVFFI9300DFWT/@@download/IGVFFI9300DFWT.fastq.gz",
"md5sum": "68c9a41837e6b61c89744d06d1563b9c",
"s3_uri": "s3://igvf-files/2023/09/05/9e1d896b-510c-4a54-9641-370f61f344fb/IGVFFI9300DFWT.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-133_L2_SS-PKR-129_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4244QAXF/",
"accession": "IGVFFI4244QAXF",
"aliases": [
"buenrostro-bernstein:SS-LS_2008_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:43.129442+00:00",
"file_format": "yaml",
"file_size": 1229,
"href": "/configuration-files/IGVFFI4244QAXF/@@download/IGVFFI4244QAXF.yaml.gz",
"md5sum": "a69d3a14ff9b4b020044d756e8fbff58",
"s3_uri": "s3://igvf-files/2024/09/17/055c2b1c-f18e-4463-9896-46ee4d94fcc1/IGVFFI4244QAXF.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2008_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3556EFAE/",
"accession": "IGVFFI3556EFAE",
"aliases": [
"buenrostro-bernstein:SS-LS_1980_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:49.673442+00:00",
"file_format": "yaml",
"file_size": 1228,
"href": "/configuration-files/IGVFFI3556EFAE/@@download/IGVFFI3556EFAE.yaml.gz",
"md5sum": "befa54504515c9c21c3debe3afda081c",
"s3_uri": "s3://igvf-files/2024/09/17/b75e066c-16f2-4c8d-9f64-fdaf841a432c/IGVFFI3556EFAE.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_1980_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/IGVFDS5192VPKQ/",
"accession": "IGVFDS5192VPKQ",
"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"
}
],
"release_timestamp": "2025-03-28T21:22:34.142101+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": "2023-09-05T19:27:49.088778+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "54d50328-a12e-4a41-9ee5-b483ff880162"
}