{
"@context": "/terms/",
"@id": "/curated-sets/IGVFDS4729GLXH/",
"@type": [
"CuratedSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4729GLXH",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-grnas-set"
],
"assemblies": [
"GRCh38"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI2489BLJI](/tabular-files/IGVFFI2489BLJI/) has `upload_status` invalidated. Validation error detail: {\"tabular_file_error\": {\"schema\": \"src/schemas/table_schemas/guide_rna_sequences.json\", \"error_number_limit\": 1000, \"number_of_errors\": 265, \"extra-label\": {\"count\": 1, \"description\": \"The header of the data source contains label that does not exist in the provided schema.\", \"details\": [{\"row_number\": null, \"field_number\": 17, \"note\": \"\"}]}, \"incorrect-label\": {\"count\": 16, \"description\": \"One of the data source header does not match the field name defined in the schema.\", \"details\": [{\"row_number\": null, \"field_number\": 1, \"note\": \"\"}, {\"row_number\": null, \"field_number\": 2, \"note\": \"\"}]}, \"type-error\": {\"count\": 136, \"description\": \"The value does not match the schema type and format for this field.\", \"details\": [{\"row_number\": 2, \"field_number\": 2, \"note\": \"type is \\\"boolean/default\\\"\"}, {\"row_number\": 2, \"field_number\": 5, \"note\": \"type is \\\"integer/default\\\"\"}]}, \"constraint-error\": {\"count\": 72, \"description\": \"A field value does not conform to a constraint.\", \"details\": [{\"row_number\": 2, \"field_number\": 3, \"note\": \"constraint \\\"enum\\\" is \\\"['safe-targeting', 'non-targeting', 'targeting', 'positive control', 'negative control', 'variant']\\\"\"}, {\"row_number\": 2, \"field_number\": 7, \"note\": \"constraint \\\"enum\\\" is \\\"['+', '-']\\\"\"}]}, \"extra-cell\": {\"count\": 40, \"description\": \"This row has more values compared to the header row (the first row in the data source). A key concept is that all the rows in tabular data must have the same number of columns.\", \"details\": [{\"row_number\": 2, \"field_number\": 17, \"note\": \"\"}, {\"row_number\": 3, \"field_number\": 17, \"note\": \"\"}]}, \"error_types\": [\"incorrect-label\", \"type-error\", \"extra-cell\", \"extra-label\", \"constraint-error\"]}}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI2489BLJI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI2489BLJI](/tabular-files/IGVFFI2489BLJI/) 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/IGVFFI2489BLJI/"
},
{
"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/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8036VPRU](/primary-cells/IGVFSM8036VPRU/) 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/IGVFSM8036VPRU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6223YCQV](/primary-cells/IGVFSM6223YCQV/) 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/IGVFSM6223YCQV/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2105CLXS](/primary-cells/IGVFSM2105CLXS/) 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/IGVFSM2105CLXS/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM5189UBOI](/primary-cells/IGVFSM5189UBOI/) 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/IGVFSM5189UBOI/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2747RJFY](/primary-cells/IGVFSM2747RJFY/) 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/IGVFSM2747RJFY/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3795JDHP](/primary-cells/IGVFSM3795JDHP/) 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/IGVFSM3795JDHP/"
}
]
},
"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"
},
"control_for": [],
"creation_timestamp": "2024-04-30T16:08:14.865921+00:00",
"file_set_type": "guide RNAs",
"files": [
{
"@id": "/tabular-files/IGVFFI1405WMSH/",
"accession": "IGVFFI1405WMSH",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-grnas-metadata"
],
"assembly": "GRCh38",
"content_type": "guide RNA sequences",
"controlled_access": false,
"creation_timestamp": "2024-04-30T17:33:39.679195+00:00",
"file_format": "tsv",
"file_size": 1383,
"href": "/tabular-files/IGVFFI1405WMSH/@@download/IGVFFI1405WMSH.tsv.gz",
"s3_uri": "s3://igvf-files/2024/04/30/5fe599e8-1f0d-437d-ba43-db082edfb8f3/IGVFFI1405WMSH.tsv.gz",
"status": "revoked",
"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",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2489BLJI/",
"accession": "IGVFFI2489BLJI",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-grnas-metadata-v3"
],
"assembly": "GRCh38",
"content_type": "guide RNA sequences",
"controlled_access": false,
"creation_timestamp": "2024-11-01T19:41:41.378701+00:00",
"file_format": "tsv",
"file_size": 1520,
"href": "/tabular-files/IGVFFI2489BLJI/@@download/IGVFFI2489BLJI.tsv.gz",
"s3_uri": "s3://igvf-files/2024/11/01/2ecf145e-5328-41a9-8d27-86584813fca6/IGVFFI2489BLJI.tsv.gz",
"status": "in progress",
"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.v3.txt.gz",
"upload_status": "invalidated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"release_timestamp": "2024-10-23T21:09:36.148600+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM8036VPRU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8036VPRU",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"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": "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/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6223YCQV",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"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": "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/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2105CLXS",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"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": "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/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3795JDHP",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"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": "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/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2747RJFY",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"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": "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/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5189UBOI",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"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": "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"
}
],
"schema_version": "8",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-04-30T17:33:39.679195+00:00",
"summary": "Homo sapiens GRCh38 guide RNAs",
"taxa": "Homo sapiens",
"uuid": "2d8ec354-8116-4b47-b49c-a911d999e242"
}