{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6108ZJGC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6108ZJGC",
"aliases": [
"buenrostro-bernstein:scRNA Lib 808"
],
"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 [IGVFDS6108ZJGC](/measurement-sets/IGVFDS6108ZJGC/) 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/IGVFDS6108ZJGC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6108ZJGC](/measurement-sets/IGVFDS6108ZJGC/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6108ZJGC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6108ZJGC](/measurement-sets/IGVFDS6108ZJGC/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6108ZJGC/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM5455KAQH](/tissues/IGVFSM5455KAQH/) 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/IGVFSM5455KAQH/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000646](/sample-terms/NTR_0000646/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000646/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6108ZJGC](/measurement-sets/IGVFDS6108ZJGC/) 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/IGVFDS6108ZJGC/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM5455KAQH](/tissues/IGVFSM5455KAQH/) 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/IGVFSM5455KAQH/"
}
]
},
"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": "2025-03-05T17:52:39.499333+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO4657FUEV/",
"accession": "IGVFDO4657FUEV",
"aliases": [
"ali-mortazavi:771_B6J_10M",
"buenrostro-bernstein:Donor 2077"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4850ICNV/",
"accession": "IGVFFI4850ICNV",
"aliases": [
"buenrostro-bernstein:SS-LS_8361_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:07.148865+00:00",
"file_format": "fastq",
"file_size": 6679996151,
"href": "/sequence-files/IGVFFI4850ICNV/@@download/IGVFFI4850ICNV.fastq.gz",
"md5sum": "b2f1c4550e0699db55ee5df3f49ab6e0",
"s3_uri": "s3://igvf-files/2025/03/05/fc57ca37-7f91-4c55-8da1-354116c90489/IGVFFI4850ICNV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2215_L7_SS-PKR-574_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1855SINJ/",
"accession": "IGVFFI1855SINJ",
"aliases": [
"buenrostro-bernstein:SS-LS_8361_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:05.032809+00:00",
"file_format": "fastq",
"file_size": 3867862345,
"href": "/sequence-files/IGVFFI1855SINJ/@@download/IGVFFI1855SINJ.fastq.gz",
"md5sum": "e4d49c60a4b1a2391fcfdca07e458c4a",
"s3_uri": "s3://igvf-files/2025/03/05/51ef5ed6-ea4b-4952-ae0c-e6a9fe30a405/IGVFFI1855SINJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2215_L7_SS-PKR-574_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7800OICN/",
"accession": "IGVFFI7800OICN",
"aliases": [
"buenrostro-bernstein:SS-LS_8321_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:36.487927+00:00",
"file_format": "fastq",
"file_size": 11826657012,
"href": "/sequence-files/IGVFFI7800OICN/@@download/IGVFFI7800OICN.fastq.gz",
"md5sum": "4218065bedbdae65768db85e7f245b4e",
"s3_uri": "s3://igvf-files/2025/03/05/ccef46bb-851d-4f27-a662-b612e8e82cd1/IGVFFI7800OICN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2175_L7_SS-PKR-574_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1077EZRS/",
"accession": "IGVFFI1077EZRS",
"aliases": [
"buenrostro-bernstein:SS-LS_8321_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:34.949148+00:00",
"file_format": "fastq",
"file_size": 6818263009,
"href": "/sequence-files/IGVFFI1077EZRS/@@download/IGVFFI1077EZRS.fastq.gz",
"md5sum": "233c6d8154ac6d57ed68025e1df08f2f",
"s3_uri": "s3://igvf-files/2025/03/05/aaf4615e-5d57-4181-878c-e506cb721fd3/IGVFFI1077EZRS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2175_L7_SS-PKR-574_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9431VAQP/",
"accession": "IGVFFI9431VAQP",
"aliases": [
"buenrostro-bernstein:SS-LS_8361_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:12.806958+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI9431VAQP/@@download/IGVFFI9431VAQP.yaml.gz",
"md5sum": "37343038c05043839299f755d43836fb",
"s3_uri": "s3://igvf-files/2025/03/07/fd0ea75b-71b5-4b9e-aa5e-42d7b9fd7068/IGVFFI9431VAQP.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8361_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5885YVDV/",
"accession": "IGVFFI5885YVDV",
"aliases": [
"buenrostro-bernstein:SS-LS_8321_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:56:56.719457+00:00",
"file_format": "yaml",
"file_size": 1285,
"href": "/configuration-files/IGVFFI5885YVDV/@@download/IGVFFI5885YVDV.yaml.gz",
"md5sum": "a22329a38d193ce3a231c8196be9170a",
"s3_uri": "s3://igvf-files/2025/03/07/f1877789-ef80-4aa8-96fb-c21af2f194e6/IGVFFI5885YVDV.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8321_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1032MMCP/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI3897QKNI/",
"/tabular-files/IGVFFI2668ZFEB/"
],
"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/IGVFDS7535KDYJ/",
"accession": "IGVFDS7535KDYJ",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:51.815750+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM5455KAQH/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5455KAQH",
"aliases": [
"buenrostro-bernstein:BioSam 5154_SS-PKR 574"
],
"cellular_sub_pool": "SS-PKR 574",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
"term_name": "left cerebral cortex"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6J (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 574)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T17:57:34.949148+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "9a1c6dbf-d8d2-4441-93da-7e73b5cae813"
}