{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
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],
"assay_titles": [
"CRISPR FACS screen"
],
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"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7030KVXG](/primary-cells/IGVFSM7030KVXG/) 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/IGVFSM7030KVXG/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6350DJQS](/primary-cells/IGVFSM6350DJQS/) 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/IGVFSM6350DJQS/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4694MBIW](/primary-cells/IGVFSM4694MBIW/) 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/IGVFSM4694MBIW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7658WDNM](/primary-cells/IGVFSM7658WDNM/) 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/IGVFSM7658WDNM/"
}
]
},
"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"
},
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{
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"accession": "IGVFFI9251ZEHU",
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"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in CD2"
}
],
"control_for": [],
"creation_timestamp": "2024-08-28T21:05:45.663803+00:00",
"donors": [
{
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"aliases": [
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],
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"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4080HFHD/",
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"aliases": [
"charles-gersbach:cd8-tcells-donor-15"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
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"accession": "IGVFFI3072IFRD",
"aliases": [
"charles-gersbach:cd8-tcells-guide-quantifications-crispri-cd2"
],
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"content_type": "fold change over control",
"controlled_access": false,
"creation_timestamp": "2024-09-05T20:24:08.189338+00:00",
"file_format": "tsv",
"file_size": 13194,
"href": "/tabular-files/IGVFFI3072IFRD/@@download/IGVFFI3072IFRD.tsv.gz",
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"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI5502YFXX/",
"accession": "IGVFFI5502YFXX",
"aliases": [
"charles-gersbach:cd8-tcells-guide-counts-crispri-cd2"
],
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"content_type": "guide quantifications",
"controlled_access": false,
"creation_timestamp": "2024-09-20T18:38:58.224458+00:00",
"file_format": "csv",
"file_size": 8070,
"href": "/tabular-files/IGVFFI5502YFXX/@@download/IGVFFI5502YFXX.csv.gz",
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"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI2317FRUV/",
"accession": "IGVFFI2317FRUV",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-cd2-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
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"creation_timestamp": "2024-10-15T18:51:12.190814+00:00",
"file_format": "bam",
"file_size": 20932549,
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"s3_uri": "s3://igvf-files/2024/10/15/8c23197c-10cf-4e87-9de0-d00f0cf35f91/IGVFFI2317FRUV.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM8-High-R2_S14.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI6108ZPCY/",
"accession": "IGVFFI6108ZPCY",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-cd2-low-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:49:19.383362+00:00",
"file_format": "bam",
"file_size": 23942994,
"href": "/alignment-files/IGVFFI6108ZPCY/@@download/IGVFFI6108ZPCY.bam",
"s3_uri": "s3://igvf-files/2024/10/15/ae04d091-bd5f-4756-b871-cbfe8abb4077/IGVFFI6108ZPCY.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM8-Low-R3_S16.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI8487IOGJ/",
"accession": "IGVFFI8487IOGJ",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-cd2-high-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:51:36.445412+00:00",
"file_format": "bam",
"file_size": 20791936,
"href": "/alignment-files/IGVFFI8487IOGJ/@@download/IGVFFI8487IOGJ.bam",
"s3_uri": "s3://igvf-files/2024/10/15/9491b447-2a0a-4429-b01a-3251c142abe4/IGVFFI8487IOGJ.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM8-High-R3_S17.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI8774OGSY/",
"accession": "IGVFFI8774OGSY",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-cd2-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:48:35.603818+00:00",
"file_format": "bam",
"file_size": 18935493,
"href": "/alignment-files/IGVFFI8774OGSY/@@download/IGVFFI8774OGSY.bam",
"s3_uri": "s3://igvf-files/2024/10/15/41bec344-a5a6-41ee-a756-01285d827826/IGVFFI8774OGSY.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM8-Low-R2_S13.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5627DEFZ/",
"accession": "IGVFDS5627DEFZ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-low-bin-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7661MIEF/",
"accession": "IGVFDS7661MIEF",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-high-bin-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5951POJU/",
"accession": "IGVFDS5951POJU",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-high-bin-rep3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4663XDBF/",
"accession": "IGVFDS4663XDBF",
"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/car-t-cell-characterization-by-flow-cytometry-c48qyzvw",
"https://www.protocols.io/view/crispri-tiling-screens-c5rby52n"
],
"publications": [
{
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"publication_identifiers": [
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"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
],
"status": "released"
}
],
"release_timestamp": "2024-11-18T21:09:06.971008+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, sorted on expression of CD2",
"samples": [
{
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"@type": [
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"Sample",
"Item"
],
"accession": "IGVFSM6350DJQS",
"aliases": [
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],
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{
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],
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{
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],
"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 CD2) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
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},
{
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"@type": [
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"Biosample",
"Sample",
"Item"
],
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],
"classifications": [
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],
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"modifications": [
{
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}
],
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{
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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 CD2 ) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7030KVXG/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
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"aliases": [
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],
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],
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"modifications": [
{
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}
],
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{
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],
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"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 CD2) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
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"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4694MBIW",
"aliases": [
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],
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],
"institutional_certificates": [],
"modifications": [
{
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}
],
"sample_terms": [
{
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"@type": [
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"OntologyTerm",
"Item"
],
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"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 CD2 ) 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": "2024-09-05T20:24:08.189338+00:00",
"summary": "CRISPR interference FACS screen targeting CD2: alignments, fold change over control, guide quantifications",
"uuid": "81129241-8f77-4be0-add3-a58742b3be6c",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow",
"status": "released"
}
]
}