{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8262FLXH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8262FLXH",
"aliases": [
"buenrostro-bernstein:scRNA Lib 843"
],
"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 [IGVFSM6880XEAH](/tissues/IGVFSM6880XEAH/) 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/IGVFSM6880XEAH/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8262FLXH](/measurement-sets/IGVFDS8262FLXH/) 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/IGVFDS8262FLXH/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8262FLXH](/measurement-sets/IGVFDS8262FLXH/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8262FLXH/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8262FLXH](/measurement-sets/IGVFDS8262FLXH/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8262FLXH/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8262FLXH](/measurement-sets/IGVFDS8262FLXH/) 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/IGVFDS8262FLXH/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6880XEAH](/tissues/IGVFSM6880XEAH/) 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/IGVFSM6880XEAH/"
}
]
},
"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": "2025-03-05T15:34:47.320864+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/IGVFFI4716BXDZ/",
"accession": "IGVFFI4716BXDZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8424_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:20.071246+00:00",
"file_format": "fastq",
"file_size": 7248213328,
"href": "/sequence-files/IGVFFI4716BXDZ/@@download/IGVFFI4716BXDZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/53411846-59e0-4872-b4d6-ccb5ad8a111a/IGVFFI4716BXDZ.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-2244_L3_SS-PKR-604_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6384SINX/",
"accession": "IGVFFI6384SINX",
"aliases": [
"buenrostro-bernstein:SS-LS_8404_R1"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:34.109689+00:00",
"file_format": "fastq",
"file_size": 4264619228,
"href": "/sequence-files/IGVFFI6384SINX/@@download/IGVFFI6384SINX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5fd3c6fc-691a-4541-b5d6-11b0f5866013/IGVFFI6384SINX.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2244_L1_SS-PKR-604_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6028FNPS/",
"accession": "IGVFFI6028FNPS",
"aliases": [
"buenrostro-bernstein:SS-LS_8414_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:55.196055+00:00",
"file_format": "fastq",
"file_size": 4245188950,
"href": "/sequence-files/IGVFFI6028FNPS/@@download/IGVFFI6028FNPS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/1015667c-cc3d-4072-ac58-e7ba2ac926bd/IGVFFI6028FNPS.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-2244_L2_SS-PKR-604_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0696CFSU/",
"accession": "IGVFFI0696CFSU",
"aliases": [
"buenrostro-bernstein:SS-LS_8404_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:36.766182+00:00",
"file_format": "fastq",
"file_size": 7284635258,
"href": "/sequence-files/IGVFFI0696CFSU/@@download/IGVFFI0696CFSU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/1bb7133f-4384-4912-8171-18560f57eae0/IGVFFI0696CFSU.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-2244_L1_SS-PKR-604_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5850KAHQ/",
"accession": "IGVFFI5850KAHQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8414_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:57.779154+00:00",
"file_format": "fastq",
"file_size": 7235059554,
"href": "/sequence-files/IGVFFI5850KAHQ/@@download/IGVFFI5850KAHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/46bd65eb-6321-4167-86e1-d229fba122f4/IGVFFI5850KAHQ.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-2244_L2_SS-PKR-604_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5063PIAD/",
"accession": "IGVFFI5063PIAD",
"aliases": [
"buenrostro-bernstein:SS-LS_8424_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:17.624790+00:00",
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"s3_uri": "s3://igvf-files/2025/03/05/abf4cd1c-0805-4e6a-8f5d-b8263c6573fd/IGVFFI5063PIAD.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2244_L3_SS-PKR-604_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2278JWUW/",
"accession": "IGVFFI2278JWUW",
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"buenrostro-bernstein:SS-LS_8424_seqspec"
],
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"creation_timestamp": "2025-03-07T19:59:05.506975+00:00",
"file_format": "yaml",
"file_size": 1289,
"href": "/configuration-files/IGVFFI2278JWUW/@@download/IGVFFI2278JWUW.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/7a91c5b1-17da-4183-897c-b4ba02603472/IGVFFI2278JWUW.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8424_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8924SHPQ/",
"accession": "IGVFFI8924SHPQ",
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"buenrostro-bernstein:SS-LS_8404_seqspec"
],
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"creation_timestamp": "2025-03-07T19:58:42.899106+00:00",
"file_format": "yaml",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8028YKVA/",
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],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8090XCBB/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
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"/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/IGVFDS6781RGTM/",
"accession": "IGVFDS6781RGTM",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:15.243848+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6880XEAH/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6880XEAH",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 604"
],
"cellular_sub_pool": "SS-PKR 604",
"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 604)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
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"title": "Siddarth Wekhande"
},
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"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "c1c8c3fd-2246-4ad2-a03c-a9dc6516b349"
}