{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4161OUYL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4161OUYL",
"aliases": [
"bradley-bernstein:scRNA Lib 128",
"buenrostro-bernstein:scRNA Lib 128"
],
"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 [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/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4161OUYL](/measurement-sets/IGVFDS4161OUYL/) 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/IGVFDS4161OUYL/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4161OUYL](/measurement-sets/IGVFDS4161OUYL/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4161OUYL/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4161OUYL](/measurement-sets/IGVFDS4161OUYL/) is missing required `strand_specificity`. Gene expression based assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS4161OUYL/"
}
],
"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": "2023-08-28T19:09:59.466729+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/IGVFFI9532ANKQ/",
"accession": "IGVFFI9532ANKQ",
"aliases": [
"bradley-bernstein:SS-LS_2069_R1",
"bradley-bernstein:SS-LS_258_R1",
"buenrostro-bernstein:SS-LS_2069_R1",
"buenrostro-bernstein:SS-LS_258_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:41.428187+00:00",
"file_format": "fastq",
"file_size": 987198150,
"href": "/sequence-files/IGVFFI9532ANKQ/@@download/IGVFFI9532ANKQ.fastq.gz",
"md5sum": "959616531def5ba317caca07076af403",
"s3_uri": "s3://igvf-files/2023/08/28/10193ec0-406e-4daf-a5b7-6c43b8472b6e/IGVFFI9532ANKQ.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-198_L1_SS-PKR-132_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6803APEV/",
"accession": "IGVFFI6803APEV",
"aliases": [
"bradley-bernstein:SS-LS_2116_R2",
"bradley-bernstein:SS-LS_268_R2",
"buenrostro-bernstein:SS-LS_2116_R2",
"buenrostro-bernstein:SS-LS_268_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:49.907809+00:00",
"file_format": "fastq",
"file_size": 1732192022,
"href": "/sequence-files/IGVFFI6803APEV/@@download/IGVFFI6803APEV.fastq.gz",
"md5sum": "501942b60ffa203286eb70de4be24e75",
"s3_uri": "s3://igvf-files/2023/08/28/7521595b-ed0d-4d6c-a0f6-301170b6758b/IGVFFI6803APEV.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-198_L2_SS-PKR-132_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4275DDIL/",
"accession": "IGVFFI4275DDIL",
"aliases": [
"bradley-bernstein:SS-LS_2069_R2",
"bradley-bernstein:SS-LS_258_R2",
"buenrostro-bernstein:SS-LS_2069_R2",
"buenrostro-bernstein:SS-LS_258_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:42.352227+00:00",
"file_format": "fastq",
"file_size": 1735486276,
"href": "/sequence-files/IGVFFI4275DDIL/@@download/IGVFFI4275DDIL.fastq.gz",
"md5sum": "bf1bab430469501985c6c1d03f6d0f9d",
"s3_uri": "s3://igvf-files/2023/08/28/94c94356-8755-48ff-ace0-2f4494be7b60/IGVFFI4275DDIL.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-198_L1_SS-PKR-132_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7523TEDF/",
"accession": "IGVFFI7523TEDF",
"aliases": [
"bradley-bernstein:SS-LS_2116_R1",
"bradley-bernstein:SS-LS_268_R1",
"buenrostro-bernstein:SS-LS_2116_R1",
"buenrostro-bernstein:SS-LS_268_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:48.955202+00:00",
"file_format": "fastq",
"file_size": 987962968,
"href": "/sequence-files/IGVFFI7523TEDF/@@download/IGVFFI7523TEDF.fastq.gz",
"md5sum": "5542b21e8bdcea7575574c654232eedb",
"s3_uri": "s3://igvf-files/2023/08/28/aaf892aa-f1d9-4cda-b098-b6761ab218f5/IGVFFI7523TEDF.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-198_L2_SS-PKR-132_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7278ACIY/",
"accession": "IGVFFI7278ACIY",
"aliases": [
"buenrostro-bernstein:SS-LS_2069_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:36.449496+00:00",
"file_format": "yaml",
"file_size": 1230,
"href": "/configuration-files/IGVFFI7278ACIY/@@download/IGVFFI7278ACIY.yaml.gz",
"md5sum": "d5b0f5000f742b8d16675f7beea7a9bc",
"s3_uri": "s3://igvf-files/2024/09/17/35410f3c-72c9-4f39-a30f-35f7b821c65c/IGVFFI7278ACIY.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2069_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1891JLQU/",
"accession": "IGVFFI1891JLQU",
"aliases": [
"buenrostro-bernstein:SS-LS_2116_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:29.409582+00:00",
"file_format": "yaml",
"file_size": 1228,
"href": "/configuration-files/IGVFFI1891JLQU/@@download/IGVFFI1891JLQU.yaml.gz",
"md5sum": "667c9f7cdbd96284bc3b6ebf0c5ecfb6",
"s3_uri": "s3://igvf-files/2024/09/17/6e13bc66-9438-4edf-b788-f8c3d1902ea1/IGVFFI1891JLQU.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2116_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/IGVFDS6721DTCZ/",
"accession": "IGVFDS6721DTCZ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7747XDUI/",
"accession": "IGVFDS7747XDUI",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8700PWZJ/",
"accession": "IGVFDS8700PWZJ",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:47.556667+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": "2023-08-28T19:11:41.428187+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "c9466fe1-aa2e-4f11-9884-60d97f28c4a0"
}