{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8364HJHL",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-crispr-ko-tfome-batf3-over"
],
"assay_titles": [
"CRISPR FACS screen"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7158ADKU](/primary-cells/IGVFSM7158ADKU/) 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/IGVFSM7158ADKU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3895SURE](/primary-cells/IGVFSM3895SURE/) 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/IGVFSM3895SURE/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8084QKPW](/primary-cells/IGVFSM8084QKPW/) 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/IGVFSM8084QKPW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7887TFLH](/primary-cells/IGVFSM7887TFLH/) 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/IGVFSM7887TFLH/"
}
]
},
"award": {
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"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"
},
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{
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"accession": "IGVFDS3667PLQB",
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"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI9735DZKB/",
"accession": "IGVFFI9735DZKB",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in many genes"
},
{
"@id": "/construct-library-sets/IGVFDS1868WXHB/",
"accession": "IGVFDS1868WXHB",
"file_set_type": "expression vector library",
"status": "released",
"summary": "expression vector library of BATF3"
}
],
"control_for": [],
"creation_timestamp": "2024-08-28T21:06:21.266508+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8306NDTY/",
"accession": "IGVFDO8306NDTY",
"aliases": [
"charles-gersbach:cd8-tcells-donor-25"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2763RVOY/",
"accession": "IGVFDO2763RVOY",
"aliases": [
"charles-gersbach:cd8-tcells-donor-26"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI8017PKLD/",
"accession": "IGVFFI8017PKLD",
"aliases": [
"charles-gersbach:cd8-tcells-guide-counts-crispr-ko-tfome-batf3-over"
],
"assembly": "custom",
"content_type": "guide quantifications",
"controlled_access": false,
"creation_timestamp": "2024-09-20T18:39:48.720891+00:00",
"file_format": "csv",
"file_size": 144399,
"href": "/tabular-files/IGVFFI8017PKLD/@@download/IGVFFI8017PKLD.csv.gz",
"s3_uri": "s3://igvf-files/2024/09/20/fdc98a24-5b01-4cad-a29b-076c14fb923c/IGVFFI8017PKLD.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPR.TFome.ko.with.BATF3.counts.table.csv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2629EIOZ/",
"accession": "IGVFFI2629EIOZ",
"aliases": [
"charles-gersbach:cd8-tcells-guide-quantifications-crispr-ko-tfome-batf3-over"
],
"assembly": "custom",
"content_type": "fold change over control",
"controlled_access": false,
"creation_timestamp": "2024-09-05T20:41:47.031556+00:00",
"file_format": "tsv",
"file_size": 375893,
"href": "/tabular-files/IGVFFI2629EIOZ/@@download/IGVFFI2629EIOZ.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/05/305c0ed2-7dbe-4a2a-8863-208209366a60/IGVFFI2629EIOZ.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/T6B_DESeq2_TFko_with_BATF3.simple.v2.txt.gz",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI1995JCIO/",
"accession": "IGVFFI1995JCIO",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:56:56.853098+00:00",
"file_format": "bam",
"file_size": 446304076,
"href": "/alignment-files/IGVFFI1995JCIO/@@download/IGVFFI1995JCIO.bam",
"s3_uri": "s3://igvf-files/2024/10/15/707adf34-3cf8-4e02-a73d-984ebe2fea50/IGVFFI1995JCIO.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_L3_S9.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI2982IKFA/",
"accession": "IGVFFI2982IKFA",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T19:02:33.513982+00:00",
"file_format": "bam",
"file_size": 473301092,
"href": "/alignment-files/IGVFFI2982IKFA/@@download/IGVFFI2982IKFA.bam",
"s3_uri": "s3://igvf-files/2024/10/15/8909a11a-3349-4d20-89e9-531b08cad315/IGVFFI2982IKFA.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_H3_S12.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5819OXDI/",
"accession": "IGVFFI5819OXDI",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-high-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T19:01:50.213063+00:00",
"file_format": "bam",
"file_size": 437309053,
"href": "/alignment-files/IGVFFI5819OXDI/@@download/IGVFFI5819OXDI.bam",
"s3_uri": "s3://igvf-files/2024/10/15/d532528a-5117-45d5-b838-672f556de1ff/IGVFFI5819OXDI.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_H2_S11.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI8725GDOS/",
"accession": "IGVFFI8725GDOS",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:56:14.664713+00:00",
"file_format": "bam",
"file_size": 379707686,
"href": "/alignment-files/IGVFFI8725GDOS/@@download/IGVFFI8725GDOS.bam",
"s3_uri": "s3://igvf-files/2024/10/15/a85afe00-bbc5-43bd-b4d2-b93065b4134b/IGVFFI8725GDOS.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_L2_S8.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS2160ZTSJ/",
"accession": "IGVFDS2160ZTSJ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-high-bin-rep1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8967NSST/",
"accession": "IGVFDS8967NSST",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-low-bin-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4325LQED/",
"accession": "IGVFDS4325LQED",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-high-bin-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3910ZTSZ/",
"accession": "IGVFDS3910ZTSZ",
"aliases": [
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],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [
"https://www.protocols.io/view/tfome-crisprko-screens-81wgbxk8olpk/v1"
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
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"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
],
"status": "released"
}
],
"release_timestamp": "2024-11-18T21:09:12.552362+00:00",
"sample_summary": "Homo sapiens CD8-positive, alpha-beta memory T primary cell primary cell, modified with CRISPRko Sp-Cas9, transfected with a expression vector library, guide library, sorted on expression of IL7R",
"samples": [
{
"@id": "/primary-cells/IGVFSM7158ADKU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7158ADKU",
"aliases": [
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],
"classifications": [
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],
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"modifications": [
{
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"modality": "knockout",
"status": "released"
}
],
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{
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"@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 (sorting details: FACS bin for 0-10% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with multiple libraries (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7887TFLH/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7887TFLH",
"aliases": [
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],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
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"modality": "knockout",
"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 (sorting details: FACS bin for 90-100% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with multiple libraries (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3895SURE/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3895SURE",
"aliases": [
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],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
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"status": "released"
}
],
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{
"@id": "/sample-terms/CL_0000909/",
"@type": [
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"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 (sorting details: FACS bin for 0-10% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with multiple libraries (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM8084QKPW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8084QKPW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-high-bin-rep1"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout",
"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 (sorting details: FACS bin for 90-100% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with multiple libraries (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": "2024-09-05T20:41:47.031556+00:00",
"summary": "CRISPR knockout FACS screen targeting IL7R: alignments, fold change over control, guide quantifications",
"uuid": "6726cb8b-7dd0-4fe2-9a33-b182b870829b",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow",
"status": "released"
}
]
}