{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS9445RJOU/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9445RJOU",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-perturb-seq-crispri"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI7101DZKK](/matrix-files/IGVFFI7101DZKK/) 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/IGVFFI7101DZKK/"
},
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI0547WZWK](/matrix-files/IGVFFI0547WZWK/) 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/IGVFFI0547WZWK/"
},
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI0296HFSP](/matrix-files/IGVFFI0296HFSP/) 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/IGVFFI0296HFSP/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM5189UBOI](/primary-cells/IGVFSM5189UBOI/) 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/IGVFSM5189UBOI/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2747RJFY](/primary-cells/IGVFSM2747RJFY/) 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/IGVFSM2747RJFY/"
},
{
"category": "unexpected workflows",
"detail": "Analysis set [IGVFDS9445RJOU](/analysis-sets/IGVFDS9445RJOU/) has multiple `workflows` linked to its files: [IGVFFI5198JCCU](/tabular-files/IGVFFI5198JCCU/), [IGVFFI9686JEQV](/tabular-files/IGVFFI9686JEQV/) link(s) to [IGVFWF5701UESO](/workflows/IGVFWF5701UESO/), [IGVFFI7101DZKK](/matrix-files/IGVFFI7101DZKK/), [IGVFFI0296HFSP](/matrix-files/IGVFFI0296HFSP/), [IGVFFI0547WZWK](/matrix-files/IGVFFI0547WZWK/) 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/IGVFDS9445RJOU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3795JDHP](/primary-cells/IGVFSM3795JDHP/) 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/IGVFSM3795JDHP/"
}
]
},
"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": "2024-10-01T15:11:07.927915+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7605NZFO/",
"accession": "IGVFDO7605NZFO",
"aliases": [
"charles-gersbach:cd8-tcells-donor-6"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@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"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI5198JCCU/",
"accession": "IGVFFI5198JCCU",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-crispri-de-mast-results"
],
"assembly": "GRCh38",
"content_type": "differential gene expression quantifications",
"controlled_access": false,
"creation_timestamp": "2024-10-01T15:05:23.923274+00:00",
"file_format": "tsv",
"file_size": 24340032,
"href": "/tabular-files/IGVFFI5198JCCU/@@download/IGVFFI5198JCCU.tsv.gz",
"s3_uri": "s3://igvf-files/2024/10/01/e958d1c4-3f62-44a0-8563-90ab9e3946e6/IGVFFI5198JCCU.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/grna.de.crispri.umi_thres_4.aggr.txt.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI7101DZKK/",
"accession": "IGVFFI7101DZKK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-mm-crispri-rep3"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-09-22T17:45:50.184331+00:00",
"file_format": "tar",
"file_size": 335261948,
"href": "/matrix-files/IGVFFI7101DZKK/@@download/IGVFFI7101DZKK.tar.gz",
"s3_uri": "s3://igvf-files/2024/09/22/8b6ab513-587c-43e7-a347-817ecfc56c35/IGVFFI7101DZKK.tar.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPRi_D3_10x.tar.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI0296HFSP/",
"accession": "IGVFFI0296HFSP",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-mm-crispri-rep1"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-09-22T17:45:10.874265+00:00",
"file_format": "tar",
"file_size": 382505366,
"href": "/matrix-files/IGVFFI0296HFSP/@@download/IGVFFI0296HFSP.tar.gz",
"s3_uri": "s3://igvf-files/2024/09/22/b9df5b53-ddfc-4aba-aa69-5f572c717d2a/IGVFFI0296HFSP.tar.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPRi_D1_10x.tar.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI0547WZWK/",
"accession": "IGVFFI0547WZWK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-mm-crispri-rep2"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-09-22T17:45:31.422125+00:00",
"file_format": "tar",
"file_size": 319017100,
"href": "/matrix-files/IGVFFI0547WZWK/@@download/IGVFFI0547WZWK.tar.gz",
"s3_uri": "s3://igvf-files/2024/09/22/3923f4ff-9049-43ab-a894-7ddc7053a786/IGVFFI0547WZWK.tar.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPRi_D2_10x.tar.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI9686JEQV/",
"accession": "IGVFFI9686JEQV",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-crispri-de-mast-results-v2"
],
"assembly": "GRCh38",
"content_type": "differential gene expression quantifications",
"controlled_access": false,
"creation_timestamp": "2025-03-25T14:23:44.300966+00:00",
"file_format": "tsv",
"file_size": 22791798,
"href": "/tabular-files/IGVFFI9686JEQV/@@download/IGVFFI9686JEQV.tsv.gz",
"s3_uri": "s3://igvf-files/2025/03/25/e74c2037-4be4-4fd8-b0ce-1ca6512fd459/IGVFFI9686JEQV.tsv.gz",
"status": "in progress",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/grna.de.crispri.umi_thres_4.aggr.v2.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS9813VHFD/",
"accession": "IGVFDS9813VHFD",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1333MBPK/",
"accession": "IGVFDS1333MBPK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9674AATW/",
"accession": "IGVFDS9674AATW",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS8029DSPH/",
"accession": "IGVFDS8029DSPH",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-grna-rep1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS2399UCGA/",
"accession": "IGVFDS2399UCGA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-grna-rep2"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS0591VNKJ/",
"accession": "IGVFDS0591VNKJ",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-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/crispri-tiling-screens-c5rby52n"
],
"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": "2024-10-18T19:50:10.406891+00:00",
"sample_summary": "Homo sapiens CD8-positive, alpha-beta memory T primary cell primary cell, modified with CRISPRi Sa-dCas9-KOX1-KRAB, transfected with a guide library",
"samples": [
{
"@id": "/primary-cells/IGVFSM5189UBOI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5189UBOI",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep3"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"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 CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3795JDHP/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3795JDHP",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep1"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"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 CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM2747RJFY/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2747RJFY",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep2"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"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 CRISPRi Sa-dCas9-KOX1-KRAB, 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": "2024-09-22T17:45:10.874265+00:00",
"summary": "interference Perturb-seq: differential gene expression quantifications, filtered feature barcode matrix",
"uuid": "1a381cc5-1cc7-44f3-8dc0-9040e30e8cd5",
"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"
}
]
}