{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
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],
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"CRISPR FACS screen"
],
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"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3073WHFV](/primary-cells/IGVFSM3073WHFV/) 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/IGVFSM3073WHFV/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4508IIAY](/primary-cells/IGVFSM4508IIAY/) 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/IGVFSM4508IIAY/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3427LEEW](/primary-cells/IGVFSM3427LEEW/) 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/IGVFSM3427LEEW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7452ZWAU](/primary-cells/IGVFSM7452ZWAU/) 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/IGVFSM7452ZWAU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1190UUKW](/primary-cells/IGVFSM1190UUKW/) 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/IGVFSM1190UUKW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6062UNTJ](/primary-cells/IGVFSM6062UNTJ/) 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/IGVFSM6062UNTJ/"
}
]
},
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"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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}
],
"status": "released",
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}
],
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"creation_timestamp": "2024-08-28T21:06:17.412292+00:00",
"donors": [
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},
{
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"status": "released",
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},
{
"@id": "/human-donors/IGVFDO8199EHWU/",
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],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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},
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"creation_timestamp": "2024-09-20T18:39:11.142942+00:00",
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},
{
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"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-High-R1_S5.sorted.bam",
"upload_status": "validated"
},
{
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"accession": "IGVFFI2031KMAC",
"aliases": [
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],
"assembly": "custom",
"content_type": "alignments",
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"creation_timestamp": "2024-10-15T18:49:53.290947+00:00",
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"file_size": 16408010,
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"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI3434RUJF/",
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"aliases": [
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"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:50:45.352217+00:00",
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"file_size": 12901267,
"href": "/alignment-files/IGVFFI3434RUJF/@@download/IGVFFI3434RUJF.bam",
"s3_uri": "s3://igvf-files/2024/10/15/3a040e6f-d013-4c4a-b5d7-574d7933ba33/IGVFFI3434RUJF.bam",
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"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-Low-R3_S10.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI4242DKSL/",
"accession": "IGVFFI4242DKSL",
"aliases": [
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],
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"creation_timestamp": "2024-10-15T18:52:40.653370+00:00",
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"s3_uri": "s3://igvf-files/2024/10/15/b5ef1cc3-392b-4056-af6b-b5ba5853cacd/IGVFFI4242DKSL.bam",
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"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5903FMQU/",
"accession": "IGVFFI5903FMQU",
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"creation_timestamp": "2024-10-15T18:53:14.452538+00:00",
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},
{
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"aliases": [
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"creation_timestamp": "2024-10-15T18:50:18.526743+00:00",
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"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-Low-R2_S7.sorted.bam",
"upload_status": "validated"
}
],
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"input_file_sets": [
{
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"accession": "IGVFDS9576VGSP",
"aliases": [
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},
{
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"accession": "IGVFDS3644PCDG",
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{
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{
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{
"@id": "/measurement-sets/IGVFDS5357XHOF/",
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"aliases": [
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},
{
"@id": "/measurement-sets/IGVFDS7534QWMG/",
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],
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}
],
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],
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}
],
"release_timestamp": "2024-11-18T21:09:14.138673+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 B2M",
"samples": [
{
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"Sample",
"Item"
],
"accession": "IGVFSM7452ZWAU",
"aliases": [
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"modifications": [
{
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],
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{
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"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 b2m) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM6062UNTJ/",
"@type": [
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"Sample",
"Item"
],
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"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [],
"modifications": [
{
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"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 (sorting details: FACS bin for 90-100% expression of b2m) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM4508IIAY/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4508IIAY",
"aliases": [
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],
"classifications": [
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],
"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 (sorting details: FACS bin for 90-100% expression of b2m) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM1190UUKW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1190UUKW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-low-bin-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"
}
],
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"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 0-10% expression of b2m) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3427LEEW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
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"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [],
"modifications": [
{
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"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
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"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 b2m) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3073WHFV/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
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"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [],
"modifications": [
{
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"modality": "interference",
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}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
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"OntologyTerm",
"Item"
],
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"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 b2m) modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
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"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-09-05T20:40:49.534517+00:00",
"summary": "CRISPR interference FACS screen targeting B2M: alignments, fold change over control, guide quantifications",
"uuid": "5552e3b5-811d-450a-8fc0-d111067cde08",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow",
"status": "released"
}
]
}