{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
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"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-rna-seq-cas-ko-znf217"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI3922QQPV](/alignment-files/IGVFFI3922QQPV/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI3922QQPV/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI3628DFGJ](/alignment-files/IGVFFI3628DFGJ/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI3628DFGJ/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI3234RYMD](/alignment-files/IGVFFI3234RYMD/) has in progress subobject reference file [IGVFFI7213AWAM](/reference-files/IGVFFI7213AWAM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI3234RYMD/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM5949AWIH](/primary-cells/IGVFSM5949AWIH/) 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/IGVFSM5949AWIH/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6537MPGY](/primary-cells/IGVFSM6537MPGY/) 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/IGVFSM6537MPGY/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0383IKGE](/primary-cells/IGVFSM0383IKGE/) 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/IGVFSM0383IKGE/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM5367RVVU](/primary-cells/IGVFSM5367RVVU/) 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/IGVFSM5367RVVU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1498WFCO](/primary-cells/IGVFSM1498WFCO/) 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/IGVFSM1498WFCO/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1311HWOF](/primary-cells/IGVFSM1311HWOF/) 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/IGVFSM1311HWOF/"
}
]
},
"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": "IGVFDS9830PJVQ",
"file_set_type": "guide library",
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"accession": "IGVFFI4223LNAY",
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"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "non-targeting guide (sgRNA) library"
},
{
"@id": "/construct-library-sets/IGVFDS7189YPQQ/",
"accession": "IGVFDS7189YPQQ",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI9240JENT/",
"accession": "IGVFFI9240JENT",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in ZNF217"
}
],
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2024-08-30T18:03:19.446690+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7589UJKG/",
"accession": "IGVFDO7589UJKG",
"aliases": [
"charles-gersbach:cd8-tcells-donor-13"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO8565PQXZ/",
"accession": "IGVFDO8565PQXZ",
"aliases": [
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],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4048LCOU/",
"accession": "IGVFDO4048LCOU",
"aliases": [
"charles-gersbach:cd8-tcells-donor-14"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI3630MMXF/",
"accession": "IGVFFI3630MMXF",
"aliases": [
"charles-gersbach:cd8-tcells-deseq2-results-rna-seq-cas-ko-znf217"
],
"assembly": "GRCh38",
"content_type": "fold change over control",
"controlled_access": false,
"creation_timestamp": "2024-09-05T20:42:24.611463+00:00",
"file_format": "tsv",
"file_size": 851521,
"href": "/tabular-files/IGVFFI3630MMXF/@@download/IGVFFI3630MMXF.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/05/2df8fe9a-6f92-48ea-991f-8e37f7ad6aa7/IGVFFI3630MMXF.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/T7A_ZNF217_KO_RNA-seq.simple.txt.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7900YIDY/",
"accession": "IGVFFI7900YIDY",
"aliases": [
"charles-gersbach:cd8-tcells-counts-rna-seq-cas-ko-znf217"
],
"assembly": "GRCh38",
"content_type": "transcript quantifications",
"controlled_access": false,
"creation_timestamp": "2024-09-20T18:40:52.856929+00:00",
"file_format": "tsv",
"file_size": 549390,
"href": "/tabular-files/IGVFFI7900YIDY/@@download/IGVFFI7900YIDY.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/20/f0c0cc67-99f3-4b02-b6a1-7052705064c9/IGVFFI7900YIDY.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.nt_znf217.star2.featurecounts.counts.txt.gz",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI3234RYMD/",
"accession": "IGVFFI3234RYMD",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-bam-rep2"
],
"assembly": "GRCh38",
"content_type": "transcriptome alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-14T21:00:42.385431+00:00",
"file_format": "bam",
"file_size": 2796982247,
"href": "/alignment-files/IGVFFI3234RYMD/@@download/IGVFFI3234RYMD.bam",
"s3_uri": "s3://igvf-files/2024/10/14/eea4d823-1547-4252-a5ef-e3ed28a3a0cd/IGVFFI3234RYMD.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.znf217.d2.star2.Aligned.out.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI3628DFGJ/",
"accession": "IGVFFI3628DFGJ",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-bam-rep1"
],
"assembly": "GRCh38",
"content_type": "transcriptome alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-14T20:59:34.263824+00:00",
"file_format": "bam",
"file_size": 2159921921,
"href": "/alignment-files/IGVFFI3628DFGJ/@@download/IGVFFI3628DFGJ.bam",
"s3_uri": "s3://igvf-files/2024/10/14/2d7652c0-a791-43fd-b7d4-3462bd9e8457/IGVFFI3628DFGJ.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.znf217.d1.star2.Aligned.out.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI3922QQPV/",
"accession": "IGVFFI3922QQPV",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-bam-rep3"
],
"assembly": "GRCh38",
"content_type": "transcriptome alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-14T21:02:00.991804+00:00",
"file_format": "bam",
"file_size": 2318584205,
"href": "/alignment-files/IGVFFI3922QQPV/@@download/IGVFFI3922QQPV.bam",
"s3_uri": "s3://igvf-files/2024/10/14/794494fb-8888-4006-8401-a7e64f46656e/IGVFFI3922QQPV.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.znf217.d3.star2.Aligned.out.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/analysis-sets/IGVFDS6924DJJC/",
"accession": "IGVFDS6924DJJC",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-cas-ko-nt"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3760HQCL/",
"accession": "IGVFDS3760HQCL",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-rep1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4636NLRL/",
"accession": "IGVFDS4636NLRL",
"aliases": [
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],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3198NMHN/",
"accession": "IGVFDS3198NMHN",
"aliases": [
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],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [],
"lab": {
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"title": "Charles Gersbach, Duke"
},
"protocols": [
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"https://www.protocols.io/view/tfome-crisprko-screens-81wgbxk8olpk/v1"
],
"publications": [
{
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"doi:10.1038/s41588-023-01554-0",
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],
"status": "released"
}
],
"release_timestamp": "2024-10-25T04:18:38.620519+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",
"samples": [
{
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"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6537MPGY",
"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [
{
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"controlled_access": false,
"status": "released"
}
],
"modifications": [
{
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"modality": "knockout",
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}
],
"sample_terms": [
{
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"@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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM5367RVVU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5367RVVU",
"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [
{
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"status": "released"
}
],
"modifications": [
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"modality": "knockout",
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}
],
"sample_terms": [
{
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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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM0383IKGE/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0383IKGE",
"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [
{
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"certificate_identifier": "IP117-01",
"controlled_access": false,
"status": "released"
}
],
"modifications": [
{
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"modality": "knockout",
"status": "released"
}
],
"sample_terms": [
{
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"@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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM5949AWIH/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5949AWIH",
"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [
{
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"controlled_access": false,
"status": "released"
}
],
"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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM1498WFCO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1498WFCO",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-nt-rep2"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
"certificate_identifier": "IP117-01",
"controlled_access": false,
"status": "released"
}
],
"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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM1311HWOF/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1311HWOF",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-znf217-rep2"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
"certificate_identifier": "IP117-01",
"controlled_access": false,
"status": "released"
}
],
"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 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": "2024-09-05T20:42:24.611463+00:00",
"summary": "knockout RNA-seq: fold change over control, transcript quantifications, transcriptome alignments",
"uuid": "bd513393-12b9-40a3-b24f-d528d7f8dc24",
"workflows": [
{
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"accession": "IGVFWF6270QWBB",
"name": "Gersbach GGR RNA-seq Pipeline",
"status": "released"
}
]
}