{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5127PEXX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5127PEXX",
"aliases": [
"buenrostro-bernstein:scRNA Lib 846"
],
"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 [IGVFSM9869JVFX](/tissues/IGVFSM9869JVFX/) 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/IGVFSM9869JVFX/"
},
{
"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 [IGVFDS5127PEXX](/measurement-sets/IGVFDS5127PEXX/) 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/IGVFDS5127PEXX/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5127PEXX](/measurement-sets/IGVFDS5127PEXX/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5127PEXX/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5127PEXX](/measurement-sets/IGVFDS5127PEXX/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5127PEXX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5127PEXX](/measurement-sets/IGVFDS5127PEXX/) 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/IGVFDS5127PEXX/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9869JVFX](/tissues/IGVFSM9869JVFX/) 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/IGVFSM9869JVFX/"
}
]
},
"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": "2025-03-05T15:34:09.740113+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": [
{
"@id": "/sequence-files/IGVFFI1818XFDW/",
"accession": "IGVFFI1818XFDW",
"aliases": [
"buenrostro-bernstein:SS-LS_8407_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:23.439538+00:00",
"file_format": "fastq",
"file_size": 9074748459,
"href": "/sequence-files/IGVFFI1818XFDW/@@download/IGVFFI1818XFDW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d8890bdf-7056-424b-9621-f56bfa4da922/IGVFFI1818XFDW.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-2247_L1_SS-PKR-607_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9581PNUC/",
"accession": "IGVFFI9581PNUC",
"aliases": [
"buenrostro-bernstein:SS-LS_8427_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:05.728540+00:00",
"file_format": "fastq",
"file_size": 9038396593,
"href": "/sequence-files/IGVFFI9581PNUC/@@download/IGVFFI9581PNUC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d6741558-4ef9-474a-9273-32715ca40817/IGVFFI9581PNUC.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-2247_L3_SS-PKR-607_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3165TPMY/",
"accession": "IGVFFI3165TPMY",
"aliases": [
"buenrostro-bernstein:SS-LS_8417_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:40.394440+00:00",
"file_format": "fastq",
"file_size": 5257550347,
"href": "/sequence-files/IGVFFI3165TPMY/@@download/IGVFFI3165TPMY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d98bbc59-1ded-4db8-b8a2-692116d9ef1a/IGVFFI3165TPMY.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-2247_L2_SS-PKR-607_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5859IQVI/",
"accession": "IGVFFI5859IQVI",
"aliases": [
"buenrostro-bernstein:SS-LS_8427_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:02.848820+00:00",
"file_format": "fastq",
"file_size": 5273197435,
"href": "/sequence-files/IGVFFI5859IQVI/@@download/IGVFFI5859IQVI.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d1b4ea93-b436-4918-8612-7cd949ad2fc1/IGVFFI5859IQVI.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-2247_L3_SS-PKR-607_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8982AHAK/",
"accession": "IGVFFI8982AHAK",
"aliases": [
"buenrostro-bernstein:SS-LS_8407_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:21.691385+00:00",
"file_format": "fastq",
"file_size": 5289612953,
"href": "/sequence-files/IGVFFI8982AHAK/@@download/IGVFFI8982AHAK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b4eb3f04-221b-430e-ada0-44cb1810709b/IGVFFI8982AHAK.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-2247_L1_SS-PKR-607_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1104NZUY/",
"accession": "IGVFFI1104NZUY",
"aliases": [
"buenrostro-bernstein:SS-LS_8417_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:42.493969+00:00",
"file_format": "fastq",
"file_size": 8995919268,
"href": "/sequence-files/IGVFFI1104NZUY/@@download/IGVFFI1104NZUY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5456bff6-33bc-453f-b050-3b7cad6e5a97/IGVFFI1104NZUY.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-2247_L2_SS-PKR-607_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7284ETTG/",
"accession": "IGVFFI7284ETTG",
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"buenrostro-bernstein:SS-LS_8417_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:40.780273+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI7284ETTG/@@download/IGVFFI7284ETTG.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/5587f936-e49f-4edb-8db9-ed23c01081f3/IGVFFI7284ETTG.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8417_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6044ZSBG/",
"accession": "IGVFFI6044ZSBG",
"aliases": [
"buenrostro-bernstein:SS-LS_8427_seqspec"
],
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"creation_timestamp": "2025-03-07T19:57:50.756004+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI6044ZSBG/@@download/IGVFFI6044ZSBG.yaml.gz",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8427_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4952COCQ/",
"accession": "IGVFFI4952COCQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8407_seqspec"
],
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8407_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2842HNUG/"
],
"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/IGVFDS9040WICU/",
"accession": "IGVFDS9040WICU",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:38.465745+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9869JVFX/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9869JVFX",
"aliases": [
"buenrostro-bernstein:BioSam 5155_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 C57BL/6J (female) left cerebral cortex tissue (cellular sub pool: SS-PKR 607)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
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"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:55:21.691385+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "26a488e5-6858-4b27-941d-b166c7325f8a"
}