{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2247EEVD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2247EEVD",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-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 in vitro system [IGVFSM1406ICND](/in-vitro-systems/IGVFSM1406ICND/) 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/IGVFSM1406ICND/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2247EEVD](/measurement-sets/IGVFDS2247EEVD/) has in progress subobject auxiliary set [IGVFDS8308NVXH](/auxiliary-sets/IGVFDS8308NVXH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2247EEVD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8308NVXH](/auxiliary-sets/IGVFDS8308NVXH/) has sequence file(s) [IGVFFI0407QZNJ](/sequence-files/IGVFFI0407QZNJ/), [IGVFFI9515GRGV](/sequence-files/IGVFFI9515GRGV/), [IGVFFI1834DQEJ](/sequence-files/IGVFFI1834DQEJ/), [IGVFFI5953FXHI](/sequence-files/IGVFFI5953FXHI/), [IGVFFI5325RCPY](/sequence-files/IGVFFI5325RCPY/), [IGVFFI3957VQYT](/sequence-files/IGVFFI3957VQYT/), [IGVFFI8497ZIRY](/sequence-files/IGVFFI8497ZIRY/), [IGVFFI6708BDAL](/sequence-files/IGVFFI6708BDAL/), [IGVFFI7351KETM](/sequence-files/IGVFFI7351KETM/), [IGVFFI0253MCNS](/sequence-files/IGVFFI0253MCNS/), [IGVFFI9031UULH](/sequence-files/IGVFFI9031UULH/), [IGVFFI7963WQDD](/sequence-files/IGVFFI7963WQDD/), [IGVFFI1276KXJX](/sequence-files/IGVFFI1276KXJX/), [IGVFFI5674MMAX](/sequence-files/IGVFFI5674MMAX/), [IGVFFI4886AIDH](/sequence-files/IGVFFI4886AIDH/), [IGVFFI4087KGHC](/sequence-files/IGVFFI4087KGHC/), [IGVFFI0544QMJM](/sequence-files/IGVFFI0544QMJM/), [IGVFFI3302LAOO](/sequence-files/IGVFFI3302LAOO/), [IGVFFI7580PJME](/sequence-files/IGVFFI7580PJME/), [IGVFFI6511OJJX](/sequence-files/IGVFFI6511OJJX/), [IGVFFI2704PCMG](/sequence-files/IGVFFI2704PCMG/), [IGVFFI0909DKEX](/sequence-files/IGVFFI0909DKEX/), [IGVFFI3177NPMW](/sequence-files/IGVFFI3177NPMW/), [IGVFFI1461EWCI](/sequence-files/IGVFFI1461EWCI/), [IGVFFI6150PWJO](/sequence-files/IGVFFI6150PWJO/), [IGVFFI8126ZAWC](/sequence-files/IGVFFI8126ZAWC/), [IGVFFI0804NXWR](/sequence-files/IGVFFI0804NXWR/), [IGVFFI2640IAHZ](/sequence-files/IGVFFI2640IAHZ/), [IGVFFI1215XWXM](/sequence-files/IGVFFI1215XWXM/), [IGVFFI4322GCVZ](/sequence-files/IGVFFI4322GCVZ/), [IGVFFI8121BRKK](/sequence-files/IGVFFI8121BRKK/), [IGVFFI9556UTBS](/sequence-files/IGVFFI9556UTBS/), [IGVFFI1336UKJI](/sequence-files/IGVFFI1336UKJI/), [IGVFFI9736SNOQ](/sequence-files/IGVFFI9736SNOQ/), [IGVFFI1008ASKE](/sequence-files/IGVFFI1008ASKE/), [IGVFFI0405WSUF](/sequence-files/IGVFFI0405WSUF/), [IGVFFI9562BVVZ](/sequence-files/IGVFFI9562BVVZ/), [IGVFFI8231VQOQ](/sequence-files/IGVFFI8231VQOQ/), [IGVFFI3968GEMM](/sequence-files/IGVFFI3968GEMM/), [IGVFFI2960WLEO](/sequence-files/IGVFFI2960WLEO/), [IGVFFI3978OMCI](/sequence-files/IGVFFI3978OMCI/), [IGVFFI4328CJOZ](/sequence-files/IGVFFI4328CJOZ/), [IGVFFI7155SXPF](/sequence-files/IGVFFI7155SXPF/), [IGVFFI6978DLPJ](/sequence-files/IGVFFI6978DLPJ/), [IGVFFI7172HGYV](/sequence-files/IGVFFI7172HGYV/), [IGVFFI2363SBJW](/sequence-files/IGVFFI2363SBJW/), [IGVFFI4206TEDQ](/sequence-files/IGVFFI4206TEDQ/), [IGVFFI8736IQSP](/sequence-files/IGVFFI8736IQSP/) 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/IGVFDS8308NVXH/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8308NVXH](/auxiliary-sets/IGVFDS8308NVXH/) has sequence file(s): [IGVFFI0407QZNJ](/sequence-files/IGVFFI0407QZNJ/), [IGVFFI9515GRGV](/sequence-files/IGVFFI9515GRGV/), [IGVFFI1834DQEJ](/sequence-files/IGVFFI1834DQEJ/), [IGVFFI5953FXHI](/sequence-files/IGVFFI5953FXHI/), [IGVFFI5325RCPY](/sequence-files/IGVFFI5325RCPY/), [IGVFFI3957VQYT](/sequence-files/IGVFFI3957VQYT/), [IGVFFI8497ZIRY](/sequence-files/IGVFFI8497ZIRY/), [IGVFFI6708BDAL](/sequence-files/IGVFFI6708BDAL/), [IGVFFI7351KETM](/sequence-files/IGVFFI7351KETM/), [IGVFFI0253MCNS](/sequence-files/IGVFFI0253MCNS/), [IGVFFI9031UULH](/sequence-files/IGVFFI9031UULH/), [IGVFFI7963WQDD](/sequence-files/IGVFFI7963WQDD/), [IGVFFI1276KXJX](/sequence-files/IGVFFI1276KXJX/), [IGVFFI5674MMAX](/sequence-files/IGVFFI5674MMAX/), [IGVFFI4886AIDH](/sequence-files/IGVFFI4886AIDH/), [IGVFFI4087KGHC](/sequence-files/IGVFFI4087KGHC/), [IGVFFI0544QMJM](/sequence-files/IGVFFI0544QMJM/), [IGVFFI3302LAOO](/sequence-files/IGVFFI3302LAOO/), [IGVFFI7580PJME](/sequence-files/IGVFFI7580PJME/), [IGVFFI6511OJJX](/sequence-files/IGVFFI6511OJJX/), [IGVFFI2704PCMG](/sequence-files/IGVFFI2704PCMG/), [IGVFFI0909DKEX](/sequence-files/IGVFFI0909DKEX/), [IGVFFI3177NPMW](/sequence-files/IGVFFI3177NPMW/), [IGVFFI1461EWCI](/sequence-files/IGVFFI1461EWCI/), [IGVFFI6150PWJO](/sequence-files/IGVFFI6150PWJO/), [IGVFFI8126ZAWC](/sequence-files/IGVFFI8126ZAWC/), [IGVFFI0804NXWR](/sequence-files/IGVFFI0804NXWR/), [IGVFFI2640IAHZ](/sequence-files/IGVFFI2640IAHZ/), [IGVFFI1215XWXM](/sequence-files/IGVFFI1215XWXM/), [IGVFFI4322GCVZ](/sequence-files/IGVFFI4322GCVZ/), [IGVFFI8121BRKK](/sequence-files/IGVFFI8121BRKK/), [IGVFFI9556UTBS](/sequence-files/IGVFFI9556UTBS/), [IGVFFI1336UKJI](/sequence-files/IGVFFI1336UKJI/), [IGVFFI9736SNOQ](/sequence-files/IGVFFI9736SNOQ/), [IGVFFI1008ASKE](/sequence-files/IGVFFI1008ASKE/), [IGVFFI0405WSUF](/sequence-files/IGVFFI0405WSUF/), [IGVFFI9562BVVZ](/sequence-files/IGVFFI9562BVVZ/), [IGVFFI8231VQOQ](/sequence-files/IGVFFI8231VQOQ/), [IGVFFI3968GEMM](/sequence-files/IGVFFI3968GEMM/), [IGVFFI2960WLEO](/sequence-files/IGVFFI2960WLEO/), [IGVFFI3978OMCI](/sequence-files/IGVFFI3978OMCI/), [IGVFFI4328CJOZ](/sequence-files/IGVFFI4328CJOZ/), [IGVFFI7155SXPF](/sequence-files/IGVFFI7155SXPF/), [IGVFFI6978DLPJ](/sequence-files/IGVFFI6978DLPJ/), [IGVFFI7172HGYV](/sequence-files/IGVFFI7172HGYV/), [IGVFFI2363SBJW](/sequence-files/IGVFFI2363SBJW/), [IGVFFI4206TEDQ](/sequence-files/IGVFFI4206TEDQ/), [IGVFFI8736IQSP](/sequence-files/IGVFFI8736IQSP/) 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/IGVFDS8308NVXH/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2247EEVD](/measurement-sets/IGVFDS2247EEVD/) 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/IGVFDS2247EEVD/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8308NVXH](/auxiliary-sets/IGVFDS8308NVXH/) 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/IGVFDS8308NVXH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8308NVXH/",
"accession": "IGVFDS8308NVXH",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-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": "2023-12-13T08:01:48.478054+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": "2023-12-20T23:07:29.656326+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1406ICND/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1406ICND",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-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": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:15:51.386854+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": "e064e18d-e803-48c9-b019-0cc8652bdec9"
}