{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7571FXYP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7571FXYP",
"aliases": [
"buenrostro-bernstein:scRNA Lib 600"
],
"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 [IGVFSM4321WQTD](/tissues/IGVFSM4321WQTD/) 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/IGVFSM4321WQTD/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7571FXYP](/measurement-sets/IGVFDS7571FXYP/) 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/IGVFDS7571FXYP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7571FXYP](/measurement-sets/IGVFDS7571FXYP/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7571FXYP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7571FXYP](/measurement-sets/IGVFDS7571FXYP/) has in progress subobject tabular file [IGVFFI9034HUWG](/tabular-files/IGVFFI9034HUWG/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7571FXYP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7571FXYP](/measurement-sets/IGVFDS7571FXYP/) 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/IGVFDS7571FXYP/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM4321WQTD](/tissues/IGVFSM4321WQTD/) 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/IGVFSM4321WQTD/"
}
]
},
"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": "2025-03-09T15:52:16.518457+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO9446AKYF/",
"accession": "IGVFDO9446AKYF",
"aliases": [
"buenrostro-bernstein:Donor 2047"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2642WOZN/",
"accession": "IGVFFI2642WOZN",
"aliases": [
"buenrostro-bernstein:SS-LS_3809_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:01:14.784831+00:00",
"file_format": "fastq",
"file_size": 917627222,
"href": "/sequence-files/IGVFFI2642WOZN/@@download/IGVFFI2642WOZN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/184e973e-4730-44d7-9da7-ef7a08573818/IGVFFI2642WOZN.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-1538_L1_SS-PKR-436_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6977ITAT/",
"accession": "IGVFFI6977ITAT",
"aliases": [
"buenrostro-bernstein:SS-LS_3833_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:00:57.446623+00:00",
"file_format": "fastq",
"file_size": 931820339,
"href": "/sequence-files/IGVFFI6977ITAT/@@download/IGVFFI6977ITAT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/a6881eba-5749-4d19-8296-ab6e8b039ce9/IGVFFI6977ITAT.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-1538_L2_SS-PKR-436_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3539IOGW/",
"accession": "IGVFFI3539IOGW",
"aliases": [
"buenrostro-bernstein:SS-LS_3809_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:01:16.230162+00:00",
"file_format": "fastq",
"file_size": 1502490214,
"href": "/sequence-files/IGVFFI3539IOGW/@@download/IGVFFI3539IOGW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/5842863b-069a-4020-ac30-a41bb663bb05/IGVFFI3539IOGW.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-1538_L1_SS-PKR-436_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2496FAKM/",
"accession": "IGVFFI2496FAKM",
"aliases": [
"buenrostro-bernstein:SS-LS_3833_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:00:58.806616+00:00",
"file_format": "fastq",
"file_size": 1534642329,
"href": "/sequence-files/IGVFFI2496FAKM/@@download/IGVFFI2496FAKM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/39e04944-dc73-477d-8e4d-339c947d140b/IGVFFI2496FAKM.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-1538_L2_SS-PKR-436_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7442LQET/",
"accession": "IGVFFI7442LQET",
"aliases": [
"buenrostro-bernstein:SS-LS_3833_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-13T17:54:26.261905+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI7442LQET/@@download/IGVFFI7442LQET.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/13/640563ca-ae89-4376-9db1-e212b680ded1/IGVFFI7442LQET.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_3833_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9238INBM/",
"accession": "IGVFFI9238INBM",
"aliases": [
"buenrostro-bernstein:SS-LS_3809_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-13T17:54:35.778425+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI9238INBM/@@download/IGVFFI9238INBM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/13/9afa7a00-b86a-4992-9b33-d9804b23dccc/IGVFFI9238INBM.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_3809_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6753PKAH/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 5,
"onlist_files": [
"/tabular-files/IGVFFI9034HUWG/",
"/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/IGVFDS4752BWME/",
"accession": "IGVFDS4752BWME",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5083GBBF/",
"accession": "IGVFDS5083GBBF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6289YQBN/",
"accession": "IGVFDS6289YQBN",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5177YHMM/",
"accession": "IGVFDS5177YHMM",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:35.413978+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM4321WQTD/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4321WQTD",
"aliases": [
"buenrostro-bernstein:BioSam 4965_SS-PKR 436"
],
"cellular_sub_pool": "SS-PKR 436",
"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 brain tissue (cellular sub pool: SS-PKR 436)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-09T16:00:57.446623+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "3a48d312-3c1c-4e8b-bcea-e8dc457227b1"
}