{
"@context": "/terms/",
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"FileSet",
"Item"
],
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"aliases": [
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],
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"CRISPR FACS screen"
],
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"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4936HKEW](/primary-cells/IGVFSM4936HKEW/) 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/IGVFSM4936HKEW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0466RHGQ](/primary-cells/IGVFSM0466RHGQ/) 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/IGVFSM0466RHGQ/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2624KTRK](/primary-cells/IGVFSM2624KTRK/) 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/IGVFSM2624KTRK/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7226CVDS](/primary-cells/IGVFSM7226CVDS/) 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/IGVFSM7226CVDS/"
}
]
},
"award": {
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"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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{
"@id": "/tabular-files/IGVFFI9735DZKB/",
"accession": "IGVFFI9735DZKB",
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"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in many genes"
}
],
"control_for": [],
"creation_timestamp": "2024-08-28T21:06:19.744257+00:00",
"donors": [
{
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"aliases": [
"charles-gersbach:cd8-tcells-donor-24"
],
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},
{
"@id": "/human-donors/IGVFDO4646JDEN/",
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"charles-gersbach:cd8-tcells-donor-23"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
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"accession": "IGVFFI9930ZUUB",
"aliases": [
"charles-gersbach:cd8-tcells-guide-counts-crispr-ko-tfome"
],
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"content_type": "guide quantifications",
"controlled_access": false,
"creation_timestamp": "2024-09-20T18:39:36.212145+00:00",
"file_format": "csv",
"file_size": 146689,
"href": "/tabular-files/IGVFFI9930ZUUB/@@download/IGVFFI9930ZUUB.csv.gz",
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"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI8007AEGC/",
"accession": "IGVFFI8007AEGC",
"aliases": [
"charles-gersbach:cd8-tcells-guide-quantifications-crispr-ko-tfome"
],
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"content_type": "fold change over control",
"controlled_access": false,
"creation_timestamp": "2024-09-05T20:41:34.067052+00:00",
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"file_size": 364239,
"href": "/tabular-files/IGVFFI8007AEGC/@@download/IGVFFI8007AEGC.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/05/4a2e7a92-4227-4152-8f80-582df772a2a2/IGVFFI8007AEGC.tsv.gz",
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"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI4092OXMN/",
"accession": "IGVFFI4092OXMN",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-low-bin-rep2"
],
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"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:55:31.970109+00:00",
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"file_size": 476837087,
"href": "/alignment-files/IGVFFI4092OXMN/@@download/IGVFFI4092OXMN.bam",
"s3_uri": "s3://igvf-files/2024/10/15/8bb48d73-3903-4214-9146-8e99ec1c3a6f/IGVFFI4092OXMN.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM73_L3_S3.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI4927HZXQ/",
"accession": "IGVFFI4927HZXQ",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T19:01:06.392524+00:00",
"file_format": "bam",
"file_size": 552006004,
"href": "/alignment-files/IGVFFI4927HZXQ/@@download/IGVFFI4927HZXQ.bam",
"s3_uri": "s3://igvf-files/2024/10/15/1602bc45-1fb1-4394-a943-f606992bd1b0/IGVFFI4927HZXQ.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM73_H3_S6.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI6153GXKL/",
"accession": "IGVFFI6153GXKL",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-low-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:54:50.923693+00:00",
"file_format": "bam",
"file_size": 549412095,
"href": "/alignment-files/IGVFFI6153GXKL/@@download/IGVFFI6153GXKL.bam",
"s3_uri": "s3://igvf-files/2024/10/15/09c388ad-161b-450a-9248-def1727380ee/IGVFFI6153GXKL.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM73_L2_S2.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI9097APHN/",
"accession": "IGVFFI9097APHN",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-high-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T19:00:23.460561+00:00",
"file_format": "bam",
"file_size": 589645922,
"href": "/alignment-files/IGVFFI9097APHN/@@download/IGVFFI9097APHN.bam",
"s3_uri": "s3://igvf-files/2024/10/15/e8397125-360f-49a1-83d8-eec87f4ce3cc/IGVFFI9097APHN.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM73_H2_S5.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS0140NIXT/",
"accession": "IGVFDS0140NIXT",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-low-bin-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7858OVUD/",
"accession": "IGVFDS7858OVUD",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-high-bin-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5130AKAZ/",
"accession": "IGVFDS5130AKAZ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-low-bin-rep1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1219SFUJ/",
"accession": "IGVFDS1219SFUJ",
"aliases": [
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],
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"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/",
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"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
],
"status": "released"
}
],
"release_timestamp": "2024-11-18T21:09:10.759708+00:00",
"sample_summary": "Homo sapiens CD8-positive, alpha-beta memory T primary cell primary cell, modified with CRISPRko Sp-Cas9, transfected with a guide library, sorted on expression of IL7R",
"samples": [
{
"@id": "/primary-cells/IGVFSM2624KTRK/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2624KTRK",
"aliases": [
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],
"classifications": [
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],
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{
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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) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM4936HKEW/",
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4936HKEW",
"aliases": [
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],
"classifications": [
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],
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{
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}
],
"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"
}
],
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"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 0-10% expression of IL7R) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7226CVDS/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7226CVDS",
"aliases": [
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],
"classifications": [
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],
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"modifications": [
{
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}
],
"sample_terms": [
{
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"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) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM0466RHGQ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0466RHGQ",
"aliases": [
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],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
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"status": "released"
}
],
"sample_terms": [
{
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"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
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}
],
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"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 90-100% expression of IL7R) modified with CRISPRko Sp-Cas9, 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": "2024-09-05T20:41:34.067052+00:00",
"summary": "CRISPR knockout FACS screen targeting IL7R: alignments, fold change over control, guide quantifications",
"uuid": "72acda8d-d611-46e5-a41a-777570e148aa",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow",
"status": "released"
}
]
}