{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS5239SBBT/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5239SBBT",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-perturb-seq-crispra"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI6124CLAF](/matrix-files/IGVFFI6124CLAF/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/matrix-files/IGVFFI6124CLAF/"
},
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI9496UPFJ](/matrix-files/IGVFFI9496UPFJ/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/matrix-files/IGVFFI9496UPFJ/"
},
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI3187CILT](/matrix-files/IGVFFI3187CILT/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/matrix-files/IGVFFI3187CILT/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6223YCQV](/primary-cells/IGVFSM6223YCQV/) 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": "/primary-cells/IGVFSM6223YCQV/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2105CLXS](/primary-cells/IGVFSM2105CLXS/) 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": "/primary-cells/IGVFSM2105CLXS/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8036VPRU](/primary-cells/IGVFSM8036VPRU/) 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": "/primary-cells/IGVFSM8036VPRU/"
},
{
"category": "unexpected workflows",
"detail": "Analysis set [IGVFDS5239SBBT](/analysis-sets/IGVFDS5239SBBT/) has multiple `workflows` linked to its files: [IGVFFI6830YLEK](/tabular-files/IGVFFI6830YLEK/), [IGVFFI7979RRUI](/tabular-files/IGVFFI7979RRUI/) link(s) to [IGVFWF5701UESO](/workflows/IGVFWF5701UESO/), [IGVFFI9496UPFJ](/matrix-files/IGVFFI9496UPFJ/), [IGVFFI6124CLAF](/matrix-files/IGVFFI6124CLAF/), [IGVFFI3187CILT](/matrix-files/IGVFFI3187CILT/) link(s) to [IGVFWF7562QXLM](/workflows/IGVFWF7562QXLM/). Analysis sets are not expected to link to more than one workflow.",
"level": 40,
"level_name": "WARNING",
"name": "audit_analysis_set_multiple_workflows",
"path": "/analysis-sets/IGVFDS5239SBBT/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0821YMMV/",
"accession": "IGVFDS0821YMMV",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI1405WMSH/",
"accession": "IGVFFI1405WMSH",
"content_type": "guide RNA sequences",
"status": "revoked",
"summary": "GRCh38 guide RNA sequences"
},
{
"@id": "/tabular-files/IGVFFI2489BLJI/",
"accession": "IGVFFI2489BLJI",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in 24 genes"
}
],
"control_for": [],
"creation_timestamp": "2024-10-01T15:11:10.725095+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO6082RNLT/",
"accession": "IGVFDO6082RNLT",
"aliases": [
"charles-gersbach:cd8-tcells-donor-7"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4425KRAT/",
"accession": "IGVFDO4425KRAT",
"aliases": [
"charles-gersbach:cd8-tcells-donor-8"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7605NZFO/",
"accession": "IGVFDO7605NZFO",
"aliases": [
"charles-gersbach:cd8-tcells-donor-6"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI6830YLEK/",
"accession": "IGVFFI6830YLEK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-crispra-de-mast-results"
],
"assembly": "GRCh38",
"content_type": "differential gene expression quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-01T15:05:01.453142+00:00",
"file_format": "tsv",
"file_size": 23487211,
"href": "/tabular-files/IGVFFI6830YLEK/@@download/IGVFFI6830YLEK.tsv.gz",
"s3_uri": "s3://igvf-files/2024/10/01/cfabf8f2-5332-4452-a521-9dcf03b952fe/IGVFFI6830YLEK.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/grna.de.crispra.umi_thres_4.aggr.txt.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI9496UPFJ/",
"accession": "IGVFFI9496UPFJ",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-mm-crispra-rep1"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-09-22T17:43:59.443698+00:00",
"file_format": "tar",
"file_size": 310187325,
"href": "/matrix-files/IGVFFI9496UPFJ/@@download/IGVFFI9496UPFJ.tar.gz",
"s3_uri": "s3://igvf-files/2024/09/22/dcaa2125-3a1d-449f-8698-16008f28f1c1/IGVFFI9496UPFJ.tar.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPRa_D1_10x.tar.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI6124CLAF/",
"accession": "IGVFFI6124CLAF",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-mm-crispra-rep3"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-09-22T17:44:52.028404+00:00",
"file_format": "tar",
"file_size": 336384580,
"href": "/matrix-files/IGVFFI6124CLAF/@@download/IGVFFI6124CLAF.tar.gz",
"s3_uri": "s3://igvf-files/2024/09/22/d1860ce5-49fc-462c-9521-d7ca898c24e7/IGVFFI6124CLAF.tar.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPRa_D3_10x.tar.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI3187CILT/",
"accession": "IGVFFI3187CILT",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-mm-crispra-rep2"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-09-22T17:44:27.973402+00:00",
"file_format": "tar",
"file_size": 408023091,
"href": "/matrix-files/IGVFFI3187CILT/@@download/IGVFFI3187CILT.tar.gz",
"s3_uri": "s3://igvf-files/2024/09/22/cdc68824-145b-464f-834c-58889c92ef93/IGVFFI3187CILT.tar.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPRa_D2_10x.tar.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7979RRUI/",
"accession": "IGVFFI7979RRUI",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-crispra-de-mast-results-v2"
],
"assembly": "GRCh38",
"content_type": "differential gene expression quantifications",
"controlled_access": false,
"creation_timestamp": "2025-03-25T14:23:42.221712+00:00",
"file_format": "tsv",
"file_size": 22022842,
"href": "/tabular-files/IGVFFI7979RRUI/@@download/IGVFFI7979RRUI.tsv.gz",
"s3_uri": "s3://igvf-files/2025/03/25/b6a996ba-2b9a-46f0-8df1-eeedde64c02b/IGVFFI7979RRUI.tsv.gz",
"status": "in progress",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/grna.de.crispra.umi_thres_4.aggr.v2.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS6764PIJI/",
"accession": "IGVFDS6764PIJI",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-gex-rep1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1675WFHV/",
"accession": "IGVFDS1675WFHV",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-gex-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0238VKNF/",
"accession": "IGVFDS0238VKNF",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-gex-rep3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS9108NLTS/",
"accession": "IGVFDS9108NLTS",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS0993OMZM/",
"accession": "IGVFDS0993OMZM",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep2"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS3945FAEL/",
"accession": "IGVFDS3945FAEL",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3"
],
"file_set_type": "gRNA sequencing",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [
"https://www.protocols.io/view/perturb-seq-characterizing-regulators-of-t-cell-fu-c5s9y6h6",
"https://www.protocols.io/view/crispra-tiling-screens-c5rfy53n"
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
],
"status": "released"
}
],
"release_timestamp": "2024-10-18T19:50:01.634631+00:00",
"sample_summary": "Homo sapiens CD8-positive, alpha-beta memory T primary cell primary cell, modified with CRISPRa Sa-dCas9-VP64, transfected with a guide library",
"samples": [
{
"@id": "/primary-cells/IGVFSM6223YCQV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6223YCQV",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep2"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM2105CLXS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2105CLXS",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep3"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM8036VPRU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8036VPRU",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep1"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-09-22T17:43:59.443698+00:00",
"summary": "activation Perturb-seq: differential gene expression quantifications, filtered feature barcode matrix",
"uuid": "a5f775f7-1681-4552-b045-6d06acb8a4ee",
"workflows": [
{
"@id": "/workflows/IGVFWF7562QXLM/",
"accession": "IGVFWF7562QXLM",
"name": "Cell Ranger Gene Count Pipeline",
"status": "released"
},
{
"@id": "/workflows/IGVFWF5701UESO/",
"accession": "IGVFWF5701UESO",
"name": "Gersbach Perturb-seq workflow",
"status": "released"
}
]
}