{
"@context": "/terms/",
"@id": "/construct-library-sets/IGVFDS6102AFVS/",
"@type": [
"ConstructLibrarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6102AFVS",
"aliases": [
"charles-gersbach:hPA-ConstructLibrarySet-perturb-seq-library"
],
"applied_to_samples": [
{
"@id": "/primary-cells/IGVFSM7138HWZK/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7138HWZK",
"aliases": [
"charles-gersbach:hPA-primary-cell-perturbseq-10xlane1"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO6921DDPB/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/703c3934-6c9b-41d0-8481-e73cc64075f7/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-2xVP64-2A-Puro"
}
],
"nucleic_acid_delivery": "lentiviral transduction",
"sample_terms": [
{
"@id": "/sample-terms/CL_0000127/",
"status": "released",
"term_name": "astrocyte"
}
],
"status": "released",
"summary": "Homo sapiens astrocyte cell treated with 10 ng/mL Neurotrophin-3, 20 ng/mL Brain-Derived Neurotrophic Factor, modified with CRISPRa Sp-dCas9-2xVP64-2A-Puro, transduced (lentivirus) with a guide library",
"treatments": [
{
"@id": "/treatments/c7e73583-b639-473f-84c4-947cdc0bd81d/",
"status": "in progress",
"summary": "Treatment of 20 ng/mL Brain-Derived Neurotrophic Factor",
"treatment_term_name": "Brain-Derived Neurotrophic Factor"
},
{
"@id": "/treatments/e23aab02-ae82-4935-85ad-1f238757f3ba/",
"status": "in progress",
"summary": "Treatment of 10 ng/mL Neurotrophin-3",
"treatment_term_name": "Neurotrophin-3"
}
]
},
{
"@id": "/primary-cells/IGVFSM2166MHKA/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2166MHKA",
"aliases": [
"charles-gersbach:hPA-primary-cell-perturbseq-10xlane4"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO6216GVYW/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/703c3934-6c9b-41d0-8481-e73cc64075f7/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-2xVP64-2A-Puro"
}
],
"nucleic_acid_delivery": "lentiviral transduction",
"sample_terms": [
{
"@id": "/sample-terms/CL_0000127/",
"status": "released",
"term_name": "astrocyte"
}
],
"status": "released",
"summary": "Homo sapiens astrocyte cell treated with 10 ng/mL Neurotrophin-3, 20 ng/mL Brain-Derived Neurotrophic Factor, modified with CRISPRa Sp-dCas9-2xVP64-2A-Puro, transduced (lentivirus) with a guide library",
"treatments": [
{
"@id": "/treatments/c7e73583-b639-473f-84c4-947cdc0bd81d/",
"status": "in progress",
"summary": "Treatment of 20 ng/mL Brain-Derived Neurotrophic Factor",
"treatment_term_name": "Brain-Derived Neurotrophic Factor"
},
{
"@id": "/treatments/e23aab02-ae82-4935-85ad-1f238757f3ba/",
"status": "in progress",
"summary": "Treatment of 10 ng/mL Neurotrophin-3",
"treatment_term_name": "Neurotrophin-3"
}
]
},
{
"@id": "/primary-cells/IGVFSM6449HHZS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6449HHZS",
"aliases": [
"charles-gersbach:hPA-primary-cell-perturbseq-10xlane2"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO6921DDPB/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/703c3934-6c9b-41d0-8481-e73cc64075f7/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-2xVP64-2A-Puro"
}
],
"nucleic_acid_delivery": "lentiviral transduction",
"sample_terms": [
{
"@id": "/sample-terms/CL_0000127/",
"status": "released",
"term_name": "astrocyte"
}
],
"status": "released",
"summary": "Homo sapiens astrocyte cell treated with 10 ng/mL Neurotrophin-3, 20 ng/mL Brain-Derived Neurotrophic Factor, modified with CRISPRa Sp-dCas9-2xVP64-2A-Puro, transduced (lentivirus) with a guide library",
"treatments": [
{
"@id": "/treatments/c7e73583-b639-473f-84c4-947cdc0bd81d/",
"status": "in progress",
"summary": "Treatment of 20 ng/mL Brain-Derived Neurotrophic Factor",
"treatment_term_name": "Brain-Derived Neurotrophic Factor"
},
{
"@id": "/treatments/e23aab02-ae82-4935-85ad-1f238757f3ba/",
"status": "in progress",
"summary": "Treatment of 10 ng/mL Neurotrophin-3",
"treatment_term_name": "Neurotrophin-3"
}
]
}
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Construct library set [IGVFDS6102AFVS](/construct-library-sets/IGVFDS6102AFVS/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/construct-library-sets/IGVFDS6102AFVS/"
},
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS6102AFVS](/construct-library-sets/IGVFDS6102AFVS/) has in progress subobject reference file [IGVFFI4279ZUTM](/reference-files/IGVFFI4279ZUTM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS6102AFVS/"
},
{
"category": "mismatched status",
"detail": "Released tabular file [IGVFFI4132CWBF](/tabular-files/IGVFFI4132CWBF/) has in progress subobject curated set [IGVFDS7723GDIK](/curated-sets/IGVFDS7723GDIK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tabular-files/IGVFFI4132CWBF/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"control_for": [],
"creation_timestamp": "2025-03-28T16:29:02.356796+00:00",
"description": "Perturb-seq CRISPRa library: gRNA library of all targeting hits (padj<.01) from the TFome screen with non-targeting gRNAs",
"documents": [
"/documents/a856c52e-db3c-4a33-8ae0-8218360819be/"
],
"file_set_type": "guide library",
"file_sets": [
"/measurement-sets/IGVFDS0886UBIB/",
"/measurement-sets/IGVFDS4521RIQF/",
"/measurement-sets/IGVFDS8404CSTN/",
"/auxiliary-sets/IGVFDS7160FCCA/",
"/auxiliary-sets/IGVFDS1645YFQD/",
"/auxiliary-sets/IGVFDS7994GDON/"
],
"files": [],
"guide_type": "sgRNA",
"input_for": [],
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4132CWBF/",
"accession": "IGVFFI4132CWBF",
"aliases": [
"charles-gersbach:hPA-tabular-perturb-seq-grnas-set"
],
"content_type": "guide RNA sequences",
"file_format": "tsv",
"status": "released",
"upload_status": "validated"
}
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"large_scale_gene_list": {
"@id": "/reference-files/IGVFFI4279ZUTM/",
"accession": "IGVFFI4279ZUTM",
"aliases": [
"charles-gersbach:reference-perturb-seq-library"
],
"status": "in progress"
},
"release_timestamp": "2025-05-16T16:07:07.704834+00:00",
"schema_version": "11",
"scope": "genes",
"selection_criteria": [
"transcription start sites"
],
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"summary": "guide (sgRNA) library targeting transcription start sites in many genes",
"tiling_modality": "sparse peaks",
"uuid": "de139a2b-c845-40b4-9062-1a42b373ebdd"
}