{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1674OUCP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1674OUCP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_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 [IGVFDS1674OUCP](/measurement-sets/IGVFDS1674OUCP/) has in progress subobject auxiliary set [IGVFDS5574RLGO](/auxiliary-sets/IGVFDS5574RLGO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1674OUCP/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5175SJIS](/in-vitro-systems/IGVFSM5175SJIS/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5175SJIS/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1674OUCP](/measurement-sets/IGVFDS1674OUCP/) 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/IGVFDS1674OUCP/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5574RLGO](/auxiliary-sets/IGVFDS5574RLGO/) has sequence file(s) [IGVFFI2751SFWM](/sequence-files/IGVFFI2751SFWM/), [IGVFFI6849EKQE](/sequence-files/IGVFFI6849EKQE/), [IGVFFI7517LZRN](/sequence-files/IGVFFI7517LZRN/), [IGVFFI5261FRGH](/sequence-files/IGVFFI5261FRGH/), [IGVFFI6064CFCZ](/sequence-files/IGVFFI6064CFCZ/), [IGVFFI4353ADRG](/sequence-files/IGVFFI4353ADRG/), [IGVFFI6449QZQS](/sequence-files/IGVFFI6449QZQS/), [IGVFFI8537GUKD](/sequence-files/IGVFFI8537GUKD/), [IGVFFI7258EDPE](/sequence-files/IGVFFI7258EDPE/), [IGVFFI8666HUSZ](/sequence-files/IGVFFI8666HUSZ/), [IGVFFI7962GJRR](/sequence-files/IGVFFI7962GJRR/), [IGVFFI0743HDYX](/sequence-files/IGVFFI0743HDYX/), [IGVFFI9792LJET](/sequence-files/IGVFFI9792LJET/), [IGVFFI1130BHXT](/sequence-files/IGVFFI1130BHXT/), [IGVFFI6394HZYT](/sequence-files/IGVFFI6394HZYT/), [IGVFFI9019KSGN](/sequence-files/IGVFFI9019KSGN/), [IGVFFI9043GWJF](/sequence-files/IGVFFI9043GWJF/), [IGVFFI9021CNLQ](/sequence-files/IGVFFI9021CNLQ/), [IGVFFI4325RPSE](/sequence-files/IGVFFI4325RPSE/), [IGVFFI2164BSLS](/sequence-files/IGVFFI2164BSLS/), [IGVFFI4121DCCA](/sequence-files/IGVFFI4121DCCA/), [IGVFFI1386LWQL](/sequence-files/IGVFFI1386LWQL/), [IGVFFI9371CZGA](/sequence-files/IGVFFI9371CZGA/), [IGVFFI4091QUCN](/sequence-files/IGVFFI4091QUCN/), [IGVFFI5678VPXX](/sequence-files/IGVFFI5678VPXX/), [IGVFFI8886MCBY](/sequence-files/IGVFFI8886MCBY/), [IGVFFI8736TVDQ](/sequence-files/IGVFFI8736TVDQ/), [IGVFFI9542KCAO](/sequence-files/IGVFFI9542KCAO/), [IGVFFI8900KHJR](/sequence-files/IGVFFI8900KHJR/), [IGVFFI5351OTLF](/sequence-files/IGVFFI5351OTLF/), [IGVFFI0214WBSJ](/sequence-files/IGVFFI0214WBSJ/), [IGVFFI1284VLMR](/sequence-files/IGVFFI1284VLMR/), [IGVFFI3363HDKQ](/sequence-files/IGVFFI3363HDKQ/), [IGVFFI8382VXTU](/sequence-files/IGVFFI8382VXTU/), [IGVFFI8765BEHK](/sequence-files/IGVFFI8765BEHK/), [IGVFFI9938QWWM](/sequence-files/IGVFFI9938QWWM/), [IGVFFI6266UDFP](/sequence-files/IGVFFI6266UDFP/), [IGVFFI1324VPBT](/sequence-files/IGVFFI1324VPBT/), [IGVFFI5400UUAG](/sequence-files/IGVFFI5400UUAG/), [IGVFFI7722NGHW](/sequence-files/IGVFFI7722NGHW/), [IGVFFI0838ASIK](/sequence-files/IGVFFI0838ASIK/), [IGVFFI7224DCNP](/sequence-files/IGVFFI7224DCNP/), [IGVFFI4322GXDN](/sequence-files/IGVFFI4322GXDN/), [IGVFFI3995QWEQ](/sequence-files/IGVFFI3995QWEQ/), [IGVFFI9794IIIZ](/sequence-files/IGVFFI9794IIIZ/), [IGVFFI6421DUIN](/sequence-files/IGVFFI6421DUIN/), [IGVFFI6351WIQM](/sequence-files/IGVFFI6351WIQM/), [IGVFFI0849TYIU](/sequence-files/IGVFFI0849TYIU/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5574RLGO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5574RLGO](/auxiliary-sets/IGVFDS5574RLGO/) has sequence file(s): [IGVFFI2751SFWM](/sequence-files/IGVFFI2751SFWM/), [IGVFFI6849EKQE](/sequence-files/IGVFFI6849EKQE/), [IGVFFI7517LZRN](/sequence-files/IGVFFI7517LZRN/), [IGVFFI5261FRGH](/sequence-files/IGVFFI5261FRGH/), [IGVFFI6064CFCZ](/sequence-files/IGVFFI6064CFCZ/), [IGVFFI4353ADRG](/sequence-files/IGVFFI4353ADRG/), [IGVFFI6449QZQS](/sequence-files/IGVFFI6449QZQS/), [IGVFFI8537GUKD](/sequence-files/IGVFFI8537GUKD/), [IGVFFI7258EDPE](/sequence-files/IGVFFI7258EDPE/), [IGVFFI8666HUSZ](/sequence-files/IGVFFI8666HUSZ/), [IGVFFI7962GJRR](/sequence-files/IGVFFI7962GJRR/), [IGVFFI0743HDYX](/sequence-files/IGVFFI0743HDYX/), [IGVFFI9792LJET](/sequence-files/IGVFFI9792LJET/), [IGVFFI1130BHXT](/sequence-files/IGVFFI1130BHXT/), [IGVFFI6394HZYT](/sequence-files/IGVFFI6394HZYT/), [IGVFFI9019KSGN](/sequence-files/IGVFFI9019KSGN/), [IGVFFI9043GWJF](/sequence-files/IGVFFI9043GWJF/), [IGVFFI9021CNLQ](/sequence-files/IGVFFI9021CNLQ/), [IGVFFI4325RPSE](/sequence-files/IGVFFI4325RPSE/), [IGVFFI2164BSLS](/sequence-files/IGVFFI2164BSLS/), [IGVFFI4121DCCA](/sequence-files/IGVFFI4121DCCA/), [IGVFFI1386LWQL](/sequence-files/IGVFFI1386LWQL/), [IGVFFI9371CZGA](/sequence-files/IGVFFI9371CZGA/), [IGVFFI4091QUCN](/sequence-files/IGVFFI4091QUCN/), [IGVFFI5678VPXX](/sequence-files/IGVFFI5678VPXX/), [IGVFFI8886MCBY](/sequence-files/IGVFFI8886MCBY/), [IGVFFI8736TVDQ](/sequence-files/IGVFFI8736TVDQ/), [IGVFFI9542KCAO](/sequence-files/IGVFFI9542KCAO/), [IGVFFI8900KHJR](/sequence-files/IGVFFI8900KHJR/), [IGVFFI5351OTLF](/sequence-files/IGVFFI5351OTLF/), [IGVFFI0214WBSJ](/sequence-files/IGVFFI0214WBSJ/), [IGVFFI1284VLMR](/sequence-files/IGVFFI1284VLMR/), [IGVFFI3363HDKQ](/sequence-files/IGVFFI3363HDKQ/), [IGVFFI8382VXTU](/sequence-files/IGVFFI8382VXTU/), [IGVFFI8765BEHK](/sequence-files/IGVFFI8765BEHK/), [IGVFFI9938QWWM](/sequence-files/IGVFFI9938QWWM/), [IGVFFI6266UDFP](/sequence-files/IGVFFI6266UDFP/), [IGVFFI1324VPBT](/sequence-files/IGVFFI1324VPBT/), [IGVFFI5400UUAG](/sequence-files/IGVFFI5400UUAG/), [IGVFFI7722NGHW](/sequence-files/IGVFFI7722NGHW/), [IGVFFI0838ASIK](/sequence-files/IGVFFI0838ASIK/), [IGVFFI7224DCNP](/sequence-files/IGVFFI7224DCNP/), [IGVFFI4322GXDN](/sequence-files/IGVFFI4322GXDN/), [IGVFFI3995QWEQ](/sequence-files/IGVFFI3995QWEQ/), [IGVFFI9794IIIZ](/sequence-files/IGVFFI9794IIIZ/), [IGVFFI6421DUIN](/sequence-files/IGVFFI6421DUIN/), [IGVFFI6351WIQM](/sequence-files/IGVFFI6351WIQM/), [IGVFFI0849TYIU](/sequence-files/IGVFFI0849TYIU/) 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/IGVFDS5574RLGO/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5574RLGO](/auxiliary-sets/IGVFDS5574RLGO/) 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_for",
"path": "/auxiliary-sets/IGVFDS5574RLGO/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5574RLGO/",
"accession": "IGVFDS5574RLGO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:58.994962+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:55.829047+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5175SJIS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5175SJIS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T22:08:44.407137+00:00",
"summary": "prime editing 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": "c77529f8-ec2c-48e2-ae55-87aad932b827"
}