{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7723OVPC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7723OVPC",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-BinA_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7723OVPC](/measurement-sets/IGVFDS7723OVPC/) has sequence file(s) [IGVFFI9191BBXD](/sequence-files/IGVFFI9191BBXD/), [IGVFFI5281TEWH](/sequence-files/IGVFFI5281TEWH/), [IGVFFI1289IQYL](/sequence-files/IGVFFI1289IQYL/), [IGVFFI8456SULG](/sequence-files/IGVFFI8456SULG/), [IGVFFI6690NIDX](/sequence-files/IGVFFI6690NIDX/), [IGVFFI4680LHLH](/sequence-files/IGVFFI4680LHLH/), [IGVFFI0571KMZO](/sequence-files/IGVFFI0571KMZO/), [IGVFFI1880WCRB](/sequence-files/IGVFFI1880WCRB/), [IGVFFI6607WXEB](/sequence-files/IGVFFI6607WXEB/), [IGVFFI8840WSRI](/sequence-files/IGVFFI8840WSRI/), [IGVFFI5515FNHI](/sequence-files/IGVFFI5515FNHI/), [IGVFFI9026SAGO](/sequence-files/IGVFFI9026SAGO/), [IGVFFI0583HHIS](/sequence-files/IGVFFI0583HHIS/), [IGVFFI3734XORT](/sequence-files/IGVFFI3734XORT/), [IGVFFI7085EEEO](/sequence-files/IGVFFI7085EEEO/), [IGVFFI1161GSIX](/sequence-files/IGVFFI1161GSIX/), [IGVFFI8690SKUA](/sequence-files/IGVFFI8690SKUA/), [IGVFFI4834EPJD](/sequence-files/IGVFFI4834EPJD/), [IGVFFI5596QPHW](/sequence-files/IGVFFI5596QPHW/), [IGVFFI3934FKCL](/sequence-files/IGVFFI3934FKCL/), [IGVFFI5711FFND](/sequence-files/IGVFFI5711FFND/), [IGVFFI6429KCWE](/sequence-files/IGVFFI6429KCWE/), [IGVFFI3126NYAW](/sequence-files/IGVFFI3126NYAW/), [IGVFFI9587TGGB](/sequence-files/IGVFFI9587TGGB/), [IGVFFI9882GZNO](/sequence-files/IGVFFI9882GZNO/), [IGVFFI1415OSPP](/sequence-files/IGVFFI1415OSPP/), [IGVFFI0780SOMN](/sequence-files/IGVFFI0780SOMN/), [IGVFFI3095RSYS](/sequence-files/IGVFFI3095RSYS/), [IGVFFI4446YVOU](/sequence-files/IGVFFI4446YVOU/), [IGVFFI2884VMCZ](/sequence-files/IGVFFI2884VMCZ/), [IGVFFI5713INXZ](/sequence-files/IGVFFI5713INXZ/), [IGVFFI7317VIWQ](/sequence-files/IGVFFI7317VIWQ/), [IGVFFI5435NDLP](/sequence-files/IGVFFI5435NDLP/), [IGVFFI5932XSTE](/sequence-files/IGVFFI5932XSTE/), [IGVFFI7651WNFO](/sequence-files/IGVFFI7651WNFO/), [IGVFFI7767OIZP](/sequence-files/IGVFFI7767OIZP/), [IGVFFI1853JQBW](/sequence-files/IGVFFI1853JQBW/), [IGVFFI9177AXZK](/sequence-files/IGVFFI9177AXZK/), [IGVFFI7645QXJK](/sequence-files/IGVFFI7645QXJK/), [IGVFFI9758GKVN](/sequence-files/IGVFFI9758GKVN/), [IGVFFI4345GCVY](/sequence-files/IGVFFI4345GCVY/), [IGVFFI6511SUIM](/sequence-files/IGVFFI6511SUIM/), [IGVFFI2313UKWW](/sequence-files/IGVFFI2313UKWW/), [IGVFFI0639FMWJ](/sequence-files/IGVFFI0639FMWJ/), [IGVFFI6563XSLJ](/sequence-files/IGVFFI6563XSLJ/), [IGVFFI7228DLQD](/sequence-files/IGVFFI7228DLQD/), [IGVFFI9582RTKF](/sequence-files/IGVFFI9582RTKF/), [IGVFFI8653TJFI](/sequence-files/IGVFFI8653TJFI/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS7723OVPC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7723OVPC](/measurement-sets/IGVFDS7723OVPC/) has sequence file(s): [IGVFFI9191BBXD](/sequence-files/IGVFFI9191BBXD/), [IGVFFI5281TEWH](/sequence-files/IGVFFI5281TEWH/), [IGVFFI1289IQYL](/sequence-files/IGVFFI1289IQYL/), [IGVFFI8456SULG](/sequence-files/IGVFFI8456SULG/), [IGVFFI6690NIDX](/sequence-files/IGVFFI6690NIDX/), [IGVFFI4680LHLH](/sequence-files/IGVFFI4680LHLH/), [IGVFFI0571KMZO](/sequence-files/IGVFFI0571KMZO/), [IGVFFI1880WCRB](/sequence-files/IGVFFI1880WCRB/), [IGVFFI6607WXEB](/sequence-files/IGVFFI6607WXEB/), [IGVFFI8840WSRI](/sequence-files/IGVFFI8840WSRI/), [IGVFFI5515FNHI](/sequence-files/IGVFFI5515FNHI/), [IGVFFI9026SAGO](/sequence-files/IGVFFI9026SAGO/), [IGVFFI0583HHIS](/sequence-files/IGVFFI0583HHIS/), [IGVFFI3734XORT](/sequence-files/IGVFFI3734XORT/), [IGVFFI7085EEEO](/sequence-files/IGVFFI7085EEEO/), [IGVFFI1161GSIX](/sequence-files/IGVFFI1161GSIX/), [IGVFFI8690SKUA](/sequence-files/IGVFFI8690SKUA/), [IGVFFI4834EPJD](/sequence-files/IGVFFI4834EPJD/), [IGVFFI5596QPHW](/sequence-files/IGVFFI5596QPHW/), [IGVFFI3934FKCL](/sequence-files/IGVFFI3934FKCL/), [IGVFFI5711FFND](/sequence-files/IGVFFI5711FFND/), [IGVFFI6429KCWE](/sequence-files/IGVFFI6429KCWE/), [IGVFFI3126NYAW](/sequence-files/IGVFFI3126NYAW/), [IGVFFI9587TGGB](/sequence-files/IGVFFI9587TGGB/), [IGVFFI9882GZNO](/sequence-files/IGVFFI9882GZNO/), [IGVFFI1415OSPP](/sequence-files/IGVFFI1415OSPP/), [IGVFFI0780SOMN](/sequence-files/IGVFFI0780SOMN/), [IGVFFI3095RSYS](/sequence-files/IGVFFI3095RSYS/), [IGVFFI4446YVOU](/sequence-files/IGVFFI4446YVOU/), [IGVFFI2884VMCZ](/sequence-files/IGVFFI2884VMCZ/), [IGVFFI5713INXZ](/sequence-files/IGVFFI5713INXZ/), [IGVFFI7317VIWQ](/sequence-files/IGVFFI7317VIWQ/), [IGVFFI5435NDLP](/sequence-files/IGVFFI5435NDLP/), [IGVFFI5932XSTE](/sequence-files/IGVFFI5932XSTE/), [IGVFFI7651WNFO](/sequence-files/IGVFFI7651WNFO/), [IGVFFI7767OIZP](/sequence-files/IGVFFI7767OIZP/), [IGVFFI1853JQBW](/sequence-files/IGVFFI1853JQBW/), [IGVFFI9177AXZK](/sequence-files/IGVFFI9177AXZK/), [IGVFFI7645QXJK](/sequence-files/IGVFFI7645QXJK/), [IGVFFI9758GKVN](/sequence-files/IGVFFI9758GKVN/), [IGVFFI4345GCVY](/sequence-files/IGVFFI4345GCVY/), [IGVFFI6511SUIM](/sequence-files/IGVFFI6511SUIM/), [IGVFFI2313UKWW](/sequence-files/IGVFFI2313UKWW/), [IGVFFI0639FMWJ](/sequence-files/IGVFFI0639FMWJ/), [IGVFFI6563XSLJ](/sequence-files/IGVFFI6563XSLJ/), [IGVFFI7228DLQD](/sequence-files/IGVFFI7228DLQD/), [IGVFFI9582RTKF](/sequence-files/IGVFFI9582RTKF/), [IGVFFI8653TJFI](/sequence-files/IGVFFI8653TJFI/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS7723OVPC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7723OVPC](/measurement-sets/IGVFDS7723OVPC/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS7723OVPC/"
}
]
},
"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"
},
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{
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"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:54:29.679478+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",
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{
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},
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},
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{
"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"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": "preview",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-26T07:56:23.146035+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"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": "e38fe8f1-a020-44d0-8cfa-5340b8eb5bbf"
}