{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1996CWLE",
"aliases": [
"buenrostro-bernstein:scRNA Lib 838"
],
"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": "Measurement set [IGVFDS1996CWLE](/measurement-sets/IGVFDS1996CWLE/) 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/IGVFDS1996CWLE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1996CWLE](/measurement-sets/IGVFDS1996CWLE/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1996CWLE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1996CWLE](/measurement-sets/IGVFDS1996CWLE/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1996CWLE/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM1137TONP](/tissues/IGVFSM1137TONP/) 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/IGVFSM1137TONP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1996CWLE](/measurement-sets/IGVFDS1996CWLE/) 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/IGVFDS1996CWLE/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1137TONP](/tissues/IGVFSM1137TONP/) 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/IGVFSM1137TONP/"
}
]
},
"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": "2025-03-05T15:34:05.155093+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3508PMXX/",
"accession": "IGVFDO3508PMXX",
"aliases": [
"ali-mortazavi:768_B6J_10F",
"buenrostro-bernstein:Donor 2078"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI4309QFKJ",
"aliases": [
"buenrostro-bernstein:SS-LS_8399_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:05.700701+00:00",
"file_format": "fastq",
"file_size": 4112639475,
"href": "/sequence-files/IGVFFI4309QFKJ/@@download/IGVFFI4309QFKJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/05c35a44-cda3-4605-808b-60676ea3671a/IGVFFI4309QFKJ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2239_L1_SS-PKR-602_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9834DRFC/",
"accession": "IGVFFI9834DRFC",
"aliases": [
"buenrostro-bernstein:SS-LS_8409_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:26.746963+00:00",
"file_format": "fastq",
"file_size": 7006350668,
"href": "/sequence-files/IGVFFI9834DRFC/@@download/IGVFFI9834DRFC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6477c091-8e63-4153-a887-baa852e638e7/IGVFFI9834DRFC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2239_L2_SS-PKR-602_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9563MKQS/",
"accession": "IGVFFI9563MKQS",
"aliases": [
"buenrostro-bernstein:SS-LS_8409_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:25.098102+00:00",
"file_format": "fastq",
"file_size": 4104294337,
"href": "/sequence-files/IGVFFI9563MKQS/@@download/IGVFFI9563MKQS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f6511482-b4f5-4655-885d-005eab9e9d5f/IGVFFI9563MKQS.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2239_L2_SS-PKR-602_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6868ANRT/",
"accession": "IGVFFI6868ANRT",
"aliases": [
"buenrostro-bernstein:SS-LS_8419_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:45.485866+00:00",
"file_format": "fastq",
"file_size": 4093388047,
"href": "/sequence-files/IGVFFI6868ANRT/@@download/IGVFFI6868ANRT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/bba90a28-263e-4f94-b3c8-218323b21af6/IGVFFI6868ANRT.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2239_L3_SS-PKR-602_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5208MUJJ/",
"accession": "IGVFFI5208MUJJ",
"aliases": [
"buenrostro-bernstein:SS-LS_8399_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:07.971410+00:00",
"file_format": "fastq",
"file_size": 7033574832,
"href": "/sequence-files/IGVFFI5208MUJJ/@@download/IGVFFI5208MUJJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/c497ed41-3d7e-4e85-bf86-16b1c1711d75/IGVFFI5208MUJJ.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-2239_L1_SS-PKR-602_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2317MXJP/",
"accession": "IGVFFI2317MXJP",
"aliases": [
"buenrostro-bernstein:SS-LS_8419_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:47.262063+00:00",
"file_format": "fastq",
"file_size": 6997687297,
"href": "/sequence-files/IGVFFI2317MXJP/@@download/IGVFFI2317MXJP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/e952695b-4d01-46d0-be5a-a4724299bf1c/IGVFFI2317MXJP.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2239_L3_SS-PKR-602_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3580TDJT/",
"accession": "IGVFFI3580TDJT",
"aliases": [
"buenrostro-bernstein:SS-LS_8419_seqspec"
],
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"creation_timestamp": "2025-03-07T19:57:42.753096+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI3580TDJT/@@download/IGVFFI3580TDJT.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/20f4b48d-2035-43b0-9a79-d830d46492b1/IGVFFI3580TDJT.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8419_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1188ULBN/",
"accession": "IGVFFI1188ULBN",
"aliases": [
"buenrostro-bernstein:SS-LS_8409_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:32.029412+00:00",
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"file_size": 1287,
"href": "/configuration-files/IGVFFI1188ULBN/@@download/IGVFFI1188ULBN.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/89365ae8-7484-4780-a20e-8c5fa05fee89/IGVFFI1188ULBN.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8409_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8515SEBS/",
"accession": "IGVFFI8515SEBS",
"aliases": [
"buenrostro-bernstein:SS-LS_8399_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:21.888333+00:00",
"file_format": "yaml",
"file_size": 1286,
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8399_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4515XRXX/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI6680XCDT/",
"/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/IGVFDS4174PVSF/",
"accession": "IGVFDS4174PVSF",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:05.920534+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1137TONP/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1137TONP",
"aliases": [
"buenrostro-bernstein:BioSam 5155_SS-PKR 602"
],
"cellular_sub_pool": "SS-PKR 602",
"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 (female) left cerebral cortex tissue (cellular sub pool: SS-PKR 602)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
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},
"submitted_files_timestamp": "2025-03-05T15:55:05.700701+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "ba58ffab-1ccd-445f-9c83-00d484a92ba7"
}