{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI1405WMSH/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI1405WMSH",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-grnas-metadata"
],
"assay_titles": [],
"assembly": "GRCh38",
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI1405WMSH](/tabular-files/IGVFFI1405WMSH/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_tabular_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI1405WMSH/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"barcode_map_for": [],
"content_md5sum": "1204d5b7f6ad2c94b3cca031b61eba54",
"content_type": "guide RNA sequences",
"controlled_access": false,
"creation_timestamp": "2024-04-30T17:33:39.679195+00:00",
"file_format": "tsv",
"file_set": {
"@id": "/curated-sets/IGVFDS4729GLXH/",
"accession": "IGVFDS4729GLXH",
"file_set_type": "guide RNAs",
"samples": [
{
"@id": "/primary-cells/IGVFSM8036VPRU/",
"accession": "IGVFSM8036VPRU",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sa-dCas9-VP64"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM6223YCQV/",
"accession": "IGVFSM6223YCQV",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sa-dCas9-VP64"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM2105CLXS/",
"accession": "IGVFSM2105CLXS",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sa-dCas9-VP64"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3795JDHP/",
"accession": "IGVFSM3795JDHP",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sa-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM2747RJFY/",
"accession": "IGVFSM2747RJFY",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sa-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM5189UBOI/",
"accession": "IGVFSM5189UBOI",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sa-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"status": "released",
"summary": "Homo sapiens GRCh38 guide RNAs",
"taxa": "Homo sapiens"
},
"file_size": 1383,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI1405WMSH/@@download/IGVFFI1405WMSH.tsv.gz",
"input_file_for": [],
"integrated_in": [
{
"@id": "/construct-library-sets/IGVFDS0821YMMV/",
"file_set_type": "guide library",
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000156127/",
"status": "released",
"symbol": "BATF"
},
{
"@id": "/genes/ENSG00000123685/",
"status": "released",
"symbol": "BATF3"
},
{
"@id": "/genes/ENSG00000134107/",
"status": "released",
"symbol": "BHLHE40"
},
{
"@id": "/genes/ENSG00000095794/",
"status": "released",
"symbol": "CREM"
},
{
"@id": "/genes/ENSG00000163508/",
"status": "released",
"symbol": "EOMES"
},
{
"@id": "/genes/ENSG00000151702/",
"status": "released",
"symbol": "FLI1"
},
{
"@id": "/genes/ENSG00000186564/",
"status": "released",
"symbol": "FOXD2"
},
{
"@id": "/genes/ENSG00000150907/",
"status": "released",
"symbol": "FOXO1"
},
{
"@id": "/genes/ENSG00000154727/",
"status": "released",
"symbol": "GABPA"
},
{
"@id": "/genes/ENSG00000177374/",
"status": "released",
"symbol": "HIC1"
},
{
"@id": "/genes/ENSG00000168310/",
"status": "released",
"symbol": "IRF2"
},
{
"@id": "/genes/ENSG00000177606/",
"status": "released",
"symbol": "JUN"
},
{
"@id": "/genes/ENSG00000118513/",
"status": "released",
"symbol": "MYB"
},
{
"@id": "/genes/ENSG00000072736/",
"status": "released",
"symbol": "NFATC3"
},
{
"@id": "/genes/ENSG00000082641/",
"status": "released",
"symbol": "NFE2L1"
},
{
"@id": "/genes/ENSG00000126368/",
"status": "released",
"symbol": "NR1D1"
},
{
"@id": "/genes/ENSG00000123358/",
"status": "released",
"symbol": "NR4A1"
},
{
"@id": "/genes/ENSG00000143190/",
"status": "released",
"symbol": "POU2F1"
},
{
"@id": "/genes/ENSG00000124782/",
"status": "released",
"symbol": "RREB1"
},
{
"@id": "/genes/ENSG00000152284/",
"status": "released",
"symbol": "TCF7L1"
},
{
"@id": "/genes/ENSG00000184517/",
"status": "released",
"symbol": "ZFP1"
},
{
"@id": "/genes/ENSG00000112182/",
"status": "released",
"symbol": "BACH2"
},
{
"@id": "/genes/ENSG00000127528/",
"status": "released",
"symbol": "KLF2"
},
{
"@id": "/genes/ENSG00000130816/",
"status": "released",
"symbol": "DNMT1"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in 24 genes"
}
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"loci_list_for": [],
"md5sum": "f274e5639a730e070638d0facf569306",
"release_timestamp": "2024-10-23T21:09:37.573392+00:00",
"revoke_detail": "This has been revoked due to not including the guide_id. The updated version can be found here: https://data.igvf.org/charles-gersbach:cd8-tcells-perturb-seq-grnas-metadata-v3/",
"s3_uri": "s3://igvf-files/2024/04/30/5fe599e8-1f0d-437d-ba43-db082edfb8f3/IGVFFI1405WMSH.tsv.gz",
"schema_version": "13",
"status": "revoked",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/reference_data/AIM_2_T_cell_project_1/TF_CRISPR_i_a.scRNAseq_screen.igvf_metadata.v2.txt.gz",
"summary": "GRCh38 guide RNA sequences",
"upload_status": "validated",
"uuid": "5fe599e8-1f0d-437d-ba43-db082edfb8f3"
}