{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4607VBYI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4607VBYI",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4607VBYI](/measurement-sets/IGVFDS4607VBYI/) has in progress subobject auxiliary set [IGVFDS5929BLRS](/auxiliary-sets/IGVFDS5929BLRS/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4607VBYI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8654CBKP](/in-vitro-systems/IGVFSM8654CBKP/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8654CBKP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5929BLRS](/auxiliary-sets/IGVFDS5929BLRS/) has sequence file(s): [IGVFFI9116KCZE](/sequence-files/IGVFFI9116KCZE/), [IGVFFI8823PPPH](/sequence-files/IGVFFI8823PPPH/), [IGVFFI9278YZLM](/sequence-files/IGVFFI9278YZLM/), [IGVFFI8535WPRB](/sequence-files/IGVFFI8535WPRB/), [IGVFFI5178OSMB](/sequence-files/IGVFFI5178OSMB/), [IGVFFI1915WRNJ](/sequence-files/IGVFFI1915WRNJ/), [IGVFFI3407NDDY](/sequence-files/IGVFFI3407NDDY/), [IGVFFI7762BNDF](/sequence-files/IGVFFI7762BNDF/), [IGVFFI7165WPIE](/sequence-files/IGVFFI7165WPIE/), [IGVFFI5499NUFW](/sequence-files/IGVFFI5499NUFW/), [IGVFFI9892AUNZ](/sequence-files/IGVFFI9892AUNZ/), [IGVFFI4268NQVA](/sequence-files/IGVFFI4268NQVA/), [IGVFFI5782OJBQ](/sequence-files/IGVFFI5782OJBQ/), [IGVFFI4940XPEA](/sequence-files/IGVFFI4940XPEA/), [IGVFFI2771BIBC](/sequence-files/IGVFFI2771BIBC/), [IGVFFI2159CKRH](/sequence-files/IGVFFI2159CKRH/), [IGVFFI9879PLDL](/sequence-files/IGVFFI9879PLDL/), [IGVFFI8702LPQC](/sequence-files/IGVFFI8702LPQC/), [IGVFFI2042OSKG](/sequence-files/IGVFFI2042OSKG/), [IGVFFI3851EEZQ](/sequence-files/IGVFFI3851EEZQ/), [IGVFFI9583EGLM](/sequence-files/IGVFFI9583EGLM/), [IGVFFI0901FCDI](/sequence-files/IGVFFI0901FCDI/), [IGVFFI4100DNIV](/sequence-files/IGVFFI4100DNIV/), [IGVFFI9975VMPG](/sequence-files/IGVFFI9975VMPG/), [IGVFFI8940MBEW](/sequence-files/IGVFFI8940MBEW/), [IGVFFI1066SCXZ](/sequence-files/IGVFFI1066SCXZ/), [IGVFFI3033HJEC](/sequence-files/IGVFFI3033HJEC/), [IGVFFI6344VMDE](/sequence-files/IGVFFI6344VMDE/), [IGVFFI8091NCVM](/sequence-files/IGVFFI8091NCVM/), [IGVFFI8636AQPQ](/sequence-files/IGVFFI8636AQPQ/), [IGVFFI3409DOPF](/sequence-files/IGVFFI3409DOPF/), [IGVFFI5255XVXG](/sequence-files/IGVFFI5255XVXG/), [IGVFFI6631HHMI](/sequence-files/IGVFFI6631HHMI/), [IGVFFI9851CITF](/sequence-files/IGVFFI9851CITF/), [IGVFFI3351KGBJ](/sequence-files/IGVFFI3351KGBJ/), [IGVFFI1789VKOW](/sequence-files/IGVFFI1789VKOW/), [IGVFFI9848XAKV](/sequence-files/IGVFFI9848XAKV/), [IGVFFI6218OIZZ](/sequence-files/IGVFFI6218OIZZ/), [IGVFFI6598RJQD](/sequence-files/IGVFFI6598RJQD/), [IGVFFI9976KWSL](/sequence-files/IGVFFI9976KWSL/), [IGVFFI9711TOSB](/sequence-files/IGVFFI9711TOSB/), [IGVFFI2547ZAPS](/sequence-files/IGVFFI2547ZAPS/), [IGVFFI7563ICEU](/sequence-files/IGVFFI7563ICEU/), [IGVFFI5501FBZH](/sequence-files/IGVFFI5501FBZH/), [IGVFFI8638SCPF](/sequence-files/IGVFFI8638SCPF/), [IGVFFI3271DFPJ](/sequence-files/IGVFFI3271DFPJ/), [IGVFFI8759ETWA](/sequence-files/IGVFFI8759ETWA/), [IGVFFI7424WHZL](/sequence-files/IGVFFI7424WHZL/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS5929BLRS/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4607VBYI](/measurement-sets/IGVFDS4607VBYI/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS4607VBYI/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5929BLRS](/auxiliary-sets/IGVFDS5929BLRS/) has sequence file(s) [IGVFFI9116KCZE](/sequence-files/IGVFFI9116KCZE/), [IGVFFI8823PPPH](/sequence-files/IGVFFI8823PPPH/), [IGVFFI9278YZLM](/sequence-files/IGVFFI9278YZLM/), [IGVFFI8535WPRB](/sequence-files/IGVFFI8535WPRB/), [IGVFFI5178OSMB](/sequence-files/IGVFFI5178OSMB/), [IGVFFI1915WRNJ](/sequence-files/IGVFFI1915WRNJ/), [IGVFFI3407NDDY](/sequence-files/IGVFFI3407NDDY/), [IGVFFI7762BNDF](/sequence-files/IGVFFI7762BNDF/), [IGVFFI7165WPIE](/sequence-files/IGVFFI7165WPIE/), [IGVFFI5499NUFW](/sequence-files/IGVFFI5499NUFW/), [IGVFFI9892AUNZ](/sequence-files/IGVFFI9892AUNZ/), [IGVFFI4268NQVA](/sequence-files/IGVFFI4268NQVA/), [IGVFFI5782OJBQ](/sequence-files/IGVFFI5782OJBQ/), [IGVFFI4940XPEA](/sequence-files/IGVFFI4940XPEA/), [IGVFFI2771BIBC](/sequence-files/IGVFFI2771BIBC/), [IGVFFI2159CKRH](/sequence-files/IGVFFI2159CKRH/), [IGVFFI9879PLDL](/sequence-files/IGVFFI9879PLDL/), [IGVFFI8702LPQC](/sequence-files/IGVFFI8702LPQC/), [IGVFFI2042OSKG](/sequence-files/IGVFFI2042OSKG/), [IGVFFI3851EEZQ](/sequence-files/IGVFFI3851EEZQ/), [IGVFFI9583EGLM](/sequence-files/IGVFFI9583EGLM/), [IGVFFI0901FCDI](/sequence-files/IGVFFI0901FCDI/), [IGVFFI4100DNIV](/sequence-files/IGVFFI4100DNIV/), [IGVFFI9975VMPG](/sequence-files/IGVFFI9975VMPG/), [IGVFFI8940MBEW](/sequence-files/IGVFFI8940MBEW/), [IGVFFI1066SCXZ](/sequence-files/IGVFFI1066SCXZ/), [IGVFFI3033HJEC](/sequence-files/IGVFFI3033HJEC/), [IGVFFI6344VMDE](/sequence-files/IGVFFI6344VMDE/), [IGVFFI8091NCVM](/sequence-files/IGVFFI8091NCVM/), [IGVFFI8636AQPQ](/sequence-files/IGVFFI8636AQPQ/), [IGVFFI3409DOPF](/sequence-files/IGVFFI3409DOPF/), [IGVFFI5255XVXG](/sequence-files/IGVFFI5255XVXG/), [IGVFFI6631HHMI](/sequence-files/IGVFFI6631HHMI/), [IGVFFI9851CITF](/sequence-files/IGVFFI9851CITF/), [IGVFFI3351KGBJ](/sequence-files/IGVFFI3351KGBJ/), [IGVFFI1789VKOW](/sequence-files/IGVFFI1789VKOW/), [IGVFFI9848XAKV](/sequence-files/IGVFFI9848XAKV/), [IGVFFI6218OIZZ](/sequence-files/IGVFFI6218OIZZ/), [IGVFFI6598RJQD](/sequence-files/IGVFFI6598RJQD/), [IGVFFI9976KWSL](/sequence-files/IGVFFI9976KWSL/), [IGVFFI9711TOSB](/sequence-files/IGVFFI9711TOSB/), [IGVFFI2547ZAPS](/sequence-files/IGVFFI2547ZAPS/), [IGVFFI7563ICEU](/sequence-files/IGVFFI7563ICEU/), [IGVFFI5501FBZH](/sequence-files/IGVFFI5501FBZH/), [IGVFFI8638SCPF](/sequence-files/IGVFFI8638SCPF/), [IGVFFI3271DFPJ](/sequence-files/IGVFFI3271DFPJ/), [IGVFFI8759ETWA](/sequence-files/IGVFFI8759ETWA/), [IGVFFI7424WHZL](/sequence-files/IGVFFI7424WHZL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5929BLRS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5929BLRS](/auxiliary-sets/IGVFDS5929BLRS/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS5929BLRS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5929BLRS/",
"accession": "IGVFDS5929BLRS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:39.009563+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS4359OODY/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:07:10.879045+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8654CBKP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8654CBKP",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T08:25:32.055548+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "b75addc9-5b0d-4bea-adb8-9476f29c7ecb"
}