{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9449UYYC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9449UYYC",
"aliases": [
"buenrostro-bernstein:scRNA Lib 847"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"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/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM0974PFBP](/tissues/IGVFSM0974PFBP/) 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/IGVFSM0974PFBP/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9449UYYC](/measurement-sets/IGVFDS9449UYYC/) 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/IGVFDS9449UYYC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9449UYYC](/measurement-sets/IGVFDS9449UYYC/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9449UYYC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9449UYYC](/measurement-sets/IGVFDS9449UYYC/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9449UYYC/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9449UYYC](/measurement-sets/IGVFDS9449UYYC/) 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/IGVFDS9449UYYC/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM0974PFBP](/tissues/IGVFSM0974PFBP/) 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/IGVFSM0974PFBP/"
}
]
},
"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": "2025-03-05T15:34:50.372417+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO8443MWJY/",
"accession": "IGVFDO8443MWJY",
"aliases": [
"ali-mortazavi:773_CASTJ_10M",
"buenrostro-bernstein:Donor 2071"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4694JRSB/",
"accession": "IGVFFI4694JRSB",
"aliases": [
"buenrostro-bernstein:SS-LS_8428_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:25.958280+00:00",
"file_format": "fastq",
"file_size": 4810070605,
"href": "/sequence-files/IGVFFI4694JRSB/@@download/IGVFFI4694JRSB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/42f8dde7-90a4-4566-b69a-fad6e3abfed5/IGVFFI4694JRSB.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-2248_L3_SS-PKR-607_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2365DYTQ/",
"accession": "IGVFFI2365DYTQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8428_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:27.705148+00:00",
"file_format": "fastq",
"file_size": 8291798142,
"href": "/sequence-files/IGVFFI2365DYTQ/@@download/IGVFFI2365DYTQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/a055040f-5da9-4e82-b421-384815ca7db9/IGVFFI2365DYTQ.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-2248_L3_SS-PKR-607_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0691RIDH/",
"accession": "IGVFFI0691RIDH",
"aliases": [
"buenrostro-bernstein:SS-LS_8418_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:04.195038+00:00",
"file_format": "fastq",
"file_size": 4800086675,
"href": "/sequence-files/IGVFFI0691RIDH/@@download/IGVFFI0691RIDH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/beebf259-c36d-4e66-9037-2486c4d185a2/IGVFFI0691RIDH.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-2248_L2_SS-PKR-607_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8689ENTE/",
"accession": "IGVFFI8689ENTE",
"aliases": [
"buenrostro-bernstein:SS-LS_8408_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:42.502937+00:00",
"file_format": "fastq",
"file_size": 4826656055,
"href": "/sequence-files/IGVFFI8689ENTE/@@download/IGVFFI8689ENTE.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/50bc4a13-7f9d-438e-9a70-9c6c1780e9b4/IGVFFI8689ENTE.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-2248_L1_SS-PKR-607_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3913BDQE/",
"accession": "IGVFFI3913BDQE",
"aliases": [
"buenrostro-bernstein:SS-LS_8408_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:44.495446+00:00",
"file_format": "fastq",
"file_size": 8329668202,
"href": "/sequence-files/IGVFFI3913BDQE/@@download/IGVFFI3913BDQE.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/ed51bb4e-95b6-4dea-921f-eb6c5be6b118/IGVFFI3913BDQE.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-2248_L1_SS-PKR-607_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0152FRUN/",
"accession": "IGVFFI0152FRUN",
"aliases": [
"buenrostro-bernstein:SS-LS_8418_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:06.304017+00:00",
"file_format": "fastq",
"file_size": 8258123587,
"href": "/sequence-files/IGVFFI0152FRUN/@@download/IGVFFI0152FRUN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9c4ccaac-e224-4f94-b744-c3ecfbd7da42/IGVFFI0152FRUN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2248_L2_SS-PKR-607_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8890KBCB/",
"accession": "IGVFFI8890KBCB",
"aliases": [
"buenrostro-bernstein:SS-LS_8408_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:46.989330+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI8890KBCB/@@download/IGVFFI8890KBCB.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/b3396c14-8b36-4bc1-96c9-417a93b0c410/IGVFFI8890KBCB.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8408_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2867QOJN/",
"accession": "IGVFFI2867QOJN",
"aliases": [
"buenrostro-bernstein:SS-LS_8428_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:09.371730+00:00",
"file_format": "yaml",
"file_size": 1289,
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8428_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8126GPHK/",
"accession": "IGVFFI8126GPHK",
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"buenrostro-bernstein:SS-LS_8418_seqspec"
],
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"creation_timestamp": "2025-03-07T19:58:57.773459+00:00",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8418_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1893AKSY/"
],
"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/IGVFDS1647SMVR/",
"accession": "IGVFDS1647SMVR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:01.016460+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM0974PFBP/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0974PFBP",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 607"
],
"cellular_sub_pool": "SS-PKR 607",
"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 CAST/EiJ (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 607)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T16:00:42.502937+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "cd52f36e-e943-420b-9cb7-0cc847ed5317"
}