{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6721DTCZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6721DTCZ",
"aliases": [
"bradley-bernstein:scRNA Lib 129",
"buenrostro-bernstein:scRNA Lib 129"
],
"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 [IGVFDS6721DTCZ](/measurement-sets/IGVFDS6721DTCZ/) 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/IGVFDS6721DTCZ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6721DTCZ](/measurement-sets/IGVFDS6721DTCZ/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6721DTCZ/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM8883WYCA](/tissues/IGVFSM8883WYCA/) 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/IGVFSM8883WYCA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6721DTCZ](/measurement-sets/IGVFDS6721DTCZ/) 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/IGVFDS6721DTCZ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8883WYCA](/tissues/IGVFSM8883WYCA/) 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/IGVFSM8883WYCA/"
}
]
},
"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": "2023-08-28T19:09:58.974630+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/IGVFFI3335XFSL/",
"accession": "IGVFFI3335XFSL",
"aliases": [
"bradley-bernstein:SS-LS_2070_R2",
"bradley-bernstein:SS-LS_257_R2",
"buenrostro-bernstein:SS-LS_2070_R2",
"buenrostro-bernstein:SS-LS_257_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:38.337434+00:00",
"file_format": "fastq",
"file_size": 2570527441,
"href": "/sequence-files/IGVFFI3335XFSL/@@download/IGVFFI3335XFSL.fastq.gz",
"md5sum": "c373c10eed391fd9b5bf1570c0651971",
"s3_uri": "s3://igvf-files/2023/08/28/eacd11e8-7d66-4f7f-aa06-f600df64abc0/IGVFFI3335XFSL.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-199_L1_SS-PKR-132_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3892BRSH/",
"accession": "IGVFFI3892BRSH",
"aliases": [
"bradley-bernstein:SS-LS_2070_R1",
"bradley-bernstein:SS-LS_257_R1",
"buenrostro-bernstein:SS-LS_2070_R1",
"buenrostro-bernstein:SS-LS_257_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:37.426049+00:00",
"file_format": "fastq",
"file_size": 1432327740,
"href": "/sequence-files/IGVFFI3892BRSH/@@download/IGVFFI3892BRSH.fastq.gz",
"md5sum": "762a4a653d55fbb36adf63b2fe289fe3",
"s3_uri": "s3://igvf-files/2023/08/28/4c3fc804-b4e4-44b9-a5ed-c5a1bd096738/IGVFFI3892BRSH.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-199_L1_SS-PKR-132_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0281YHNG/",
"accession": "IGVFFI0281YHNG",
"aliases": [
"bradley-bernstein:SS-LS_2117_R1",
"bradley-bernstein:SS-LS_267_R1",
"buenrostro-bernstein:SS-LS_2117_R1",
"buenrostro-bernstein:SS-LS_267_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:39.291888+00:00",
"file_format": "fastq",
"file_size": 1434035996,
"href": "/sequence-files/IGVFFI0281YHNG/@@download/IGVFFI0281YHNG.fastq.gz",
"md5sum": "c4a240e392e869956bb6f025c4e4c767",
"s3_uri": "s3://igvf-files/2023/08/28/b63f15b3-50c0-41de-a95a-18e20bbbc69a/IGVFFI0281YHNG.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-199_L2_SS-PKR-132_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4886JZDI/",
"accession": "IGVFFI4886JZDI",
"aliases": [
"bradley-bernstein:SS-LS_2117_R2",
"bradley-bernstein:SS-LS_267_R2",
"buenrostro-bernstein:SS-LS_2117_R2",
"buenrostro-bernstein:SS-LS_267_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:40.193980+00:00",
"file_format": "fastq",
"file_size": 2566966446,
"href": "/sequence-files/IGVFFI4886JZDI/@@download/IGVFFI4886JZDI.fastq.gz",
"md5sum": "abc1308b24d25a2691f053c07ba7afa8",
"s3_uri": "s3://igvf-files/2023/08/28/f8e92e72-f8f5-4313-9420-dca08267d4b6/IGVFFI4886JZDI.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-199_L2_SS-PKR-132_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9218ORYZ/",
"accession": "IGVFFI9218ORYZ",
"aliases": [
"buenrostro-bernstein:SS-LS_2117_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:28.063206+00:00",
"file_format": "yaml",
"file_size": 1231,
"href": "/configuration-files/IGVFFI9218ORYZ/@@download/IGVFFI9218ORYZ.yaml.gz",
"md5sum": "33a9aaec92aa09ab1ffcbf017097e4b1",
"s3_uri": "s3://igvf-files/2024/09/17/1318ec1d-3d25-468e-ad31-6585ae3ff6f8/IGVFFI9218ORYZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2117_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2395FWQZ/",
"accession": "IGVFFI2395FWQZ",
"aliases": [
"buenrostro-bernstein:SS-LS_2070_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:35.365974+00:00",
"file_format": "yaml",
"file_size": 1229,
"href": "/configuration-files/IGVFFI2395FWQZ/@@download/IGVFFI2395FWQZ.yaml.gz",
"md5sum": "a7d23742837003e9143acd709f91451f",
"s3_uri": "s3://igvf-files/2024/09/17/91f2105c-306f-4ff4-ac0c-58287e09e878/IGVFFI2395FWQZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2070_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4769QTGM/"
],
"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/IGVFDS9620KXMW/",
"accession": "IGVFDS9620KXMW",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9728TWXO/",
"accession": "IGVFDS9728TWXO",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7747XDUI/",
"accession": "IGVFDS7747XDUI",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8700PWZJ/",
"accession": "IGVFDS8700PWZJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4161OUYL/",
"accession": "IGVFDS4161OUYL",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:51.049545+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM8883WYCA/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8883WYCA",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 132",
"buenrostro-bernstein:BioSam 4561_SS-PKR 132"
],
"cellular_sub_pool": "SS-PKR 132",
"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 132)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T19:11:37.426049+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "9447c8e2-49d3-4e9f-a0c9-a44f23456482"
}