{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9746QVGD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9746QVGD",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-BinD_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 [IGVFDS9746QVGD](/measurement-sets/IGVFDS9746QVGD/) has sequence file(s) [IGVFFI6817QPHU](/sequence-files/IGVFFI6817QPHU/), [IGVFFI3070ARNB](/sequence-files/IGVFFI3070ARNB/), [IGVFFI9507PNXQ](/sequence-files/IGVFFI9507PNXQ/), [IGVFFI1458COIV](/sequence-files/IGVFFI1458COIV/), [IGVFFI3108NXCH](/sequence-files/IGVFFI3108NXCH/), [IGVFFI6990ZTYO](/sequence-files/IGVFFI6990ZTYO/), [IGVFFI7366DTAL](/sequence-files/IGVFFI7366DTAL/), [IGVFFI6885CJON](/sequence-files/IGVFFI6885CJON/), [IGVFFI4763URXC](/sequence-files/IGVFFI4763URXC/), [IGVFFI7835ULKM](/sequence-files/IGVFFI7835ULKM/), [IGVFFI9337UVFB](/sequence-files/IGVFFI9337UVFB/), [IGVFFI4008IUHG](/sequence-files/IGVFFI4008IUHG/), [IGVFFI4232DESQ](/sequence-files/IGVFFI4232DESQ/), [IGVFFI6519HDDU](/sequence-files/IGVFFI6519HDDU/), [IGVFFI1077PJEO](/sequence-files/IGVFFI1077PJEO/), [IGVFFI1997RAII](/sequence-files/IGVFFI1997RAII/), [IGVFFI0207DIKQ](/sequence-files/IGVFFI0207DIKQ/), [IGVFFI4161URHQ](/sequence-files/IGVFFI4161URHQ/), [IGVFFI2749MOPN](/sequence-files/IGVFFI2749MOPN/), [IGVFFI8231DLZH](/sequence-files/IGVFFI8231DLZH/), [IGVFFI7009DEHM](/sequence-files/IGVFFI7009DEHM/), [IGVFFI8668RXCC](/sequence-files/IGVFFI8668RXCC/), [IGVFFI1127NLNN](/sequence-files/IGVFFI1127NLNN/), [IGVFFI3151HURO](/sequence-files/IGVFFI3151HURO/), [IGVFFI5667NDLO](/sequence-files/IGVFFI5667NDLO/), [IGVFFI6431NIEN](/sequence-files/IGVFFI6431NIEN/), [IGVFFI2221KGNA](/sequence-files/IGVFFI2221KGNA/), [IGVFFI8708CQFD](/sequence-files/IGVFFI8708CQFD/), [IGVFFI2028SBXI](/sequence-files/IGVFFI2028SBXI/), [IGVFFI0347OCUI](/sequence-files/IGVFFI0347OCUI/), [IGVFFI2074PZQA](/sequence-files/IGVFFI2074PZQA/), [IGVFFI7146MRMO](/sequence-files/IGVFFI7146MRMO/), [IGVFFI8567EMRA](/sequence-files/IGVFFI8567EMRA/), [IGVFFI1798VFUW](/sequence-files/IGVFFI1798VFUW/), [IGVFFI2407GGCR](/sequence-files/IGVFFI2407GGCR/), [IGVFFI9845TRGZ](/sequence-files/IGVFFI9845TRGZ/), [IGVFFI1326LCNP](/sequence-files/IGVFFI1326LCNP/), [IGVFFI7244ISCG](/sequence-files/IGVFFI7244ISCG/), [IGVFFI9424TYHU](/sequence-files/IGVFFI9424TYHU/), [IGVFFI0230VONJ](/sequence-files/IGVFFI0230VONJ/), [IGVFFI9976THOF](/sequence-files/IGVFFI9976THOF/), [IGVFFI3228JNPV](/sequence-files/IGVFFI3228JNPV/), [IGVFFI5283JKPS](/sequence-files/IGVFFI5283JKPS/), [IGVFFI7369WTPM](/sequence-files/IGVFFI7369WTPM/), [IGVFFI4731ZCOO](/sequence-files/IGVFFI4731ZCOO/), [IGVFFI6558EBBC](/sequence-files/IGVFFI6558EBBC/), [IGVFFI2839BPHP](/sequence-files/IGVFFI2839BPHP/), [IGVFFI6686VRFZ](/sequence-files/IGVFFI6686VRFZ/) 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/IGVFDS9746QVGD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9746QVGD](/measurement-sets/IGVFDS9746QVGD/) has sequence file(s): [IGVFFI6817QPHU](/sequence-files/IGVFFI6817QPHU/), [IGVFFI3070ARNB](/sequence-files/IGVFFI3070ARNB/), [IGVFFI9507PNXQ](/sequence-files/IGVFFI9507PNXQ/), [IGVFFI1458COIV](/sequence-files/IGVFFI1458COIV/), [IGVFFI3108NXCH](/sequence-files/IGVFFI3108NXCH/), [IGVFFI6990ZTYO](/sequence-files/IGVFFI6990ZTYO/), [IGVFFI7366DTAL](/sequence-files/IGVFFI7366DTAL/), [IGVFFI6885CJON](/sequence-files/IGVFFI6885CJON/), [IGVFFI4763URXC](/sequence-files/IGVFFI4763URXC/), [IGVFFI7835ULKM](/sequence-files/IGVFFI7835ULKM/), [IGVFFI9337UVFB](/sequence-files/IGVFFI9337UVFB/), [IGVFFI4008IUHG](/sequence-files/IGVFFI4008IUHG/), [IGVFFI4232DESQ](/sequence-files/IGVFFI4232DESQ/), [IGVFFI6519HDDU](/sequence-files/IGVFFI6519HDDU/), [IGVFFI1077PJEO](/sequence-files/IGVFFI1077PJEO/), [IGVFFI1997RAII](/sequence-files/IGVFFI1997RAII/), [IGVFFI0207DIKQ](/sequence-files/IGVFFI0207DIKQ/), [IGVFFI4161URHQ](/sequence-files/IGVFFI4161URHQ/), [IGVFFI2749MOPN](/sequence-files/IGVFFI2749MOPN/), [IGVFFI8231DLZH](/sequence-files/IGVFFI8231DLZH/), [IGVFFI7009DEHM](/sequence-files/IGVFFI7009DEHM/), [IGVFFI8668RXCC](/sequence-files/IGVFFI8668RXCC/), [IGVFFI1127NLNN](/sequence-files/IGVFFI1127NLNN/), [IGVFFI3151HURO](/sequence-files/IGVFFI3151HURO/), [IGVFFI5667NDLO](/sequence-files/IGVFFI5667NDLO/), [IGVFFI6431NIEN](/sequence-files/IGVFFI6431NIEN/), [IGVFFI2221KGNA](/sequence-files/IGVFFI2221KGNA/), [IGVFFI8708CQFD](/sequence-files/IGVFFI8708CQFD/), [IGVFFI2028SBXI](/sequence-files/IGVFFI2028SBXI/), [IGVFFI0347OCUI](/sequence-files/IGVFFI0347OCUI/), [IGVFFI2074PZQA](/sequence-files/IGVFFI2074PZQA/), [IGVFFI7146MRMO](/sequence-files/IGVFFI7146MRMO/), [IGVFFI8567EMRA](/sequence-files/IGVFFI8567EMRA/), [IGVFFI1798VFUW](/sequence-files/IGVFFI1798VFUW/), [IGVFFI2407GGCR](/sequence-files/IGVFFI2407GGCR/), [IGVFFI9845TRGZ](/sequence-files/IGVFFI9845TRGZ/), [IGVFFI1326LCNP](/sequence-files/IGVFFI1326LCNP/), [IGVFFI7244ISCG](/sequence-files/IGVFFI7244ISCG/), [IGVFFI9424TYHU](/sequence-files/IGVFFI9424TYHU/), [IGVFFI0230VONJ](/sequence-files/IGVFFI0230VONJ/), [IGVFFI9976THOF](/sequence-files/IGVFFI9976THOF/), [IGVFFI3228JNPV](/sequence-files/IGVFFI3228JNPV/), [IGVFFI5283JKPS](/sequence-files/IGVFFI5283JKPS/), [IGVFFI7369WTPM](/sequence-files/IGVFFI7369WTPM/), [IGVFFI4731ZCOO](/sequence-files/IGVFFI4731ZCOO/), [IGVFFI6558EBBC](/sequence-files/IGVFFI6558EBBC/), [IGVFFI2839BPHP](/sequence-files/IGVFFI2839BPHP/), [IGVFFI6686VRFZ](/sequence-files/IGVFFI6686VRFZ/) 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/IGVFDS9746QVGD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9746QVGD](/measurement-sets/IGVFDS9746QVGD/) 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/IGVFDS9746QVGD/"
}
]
},
"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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{
"@id": "/measurement-sets/IGVFDS4103BJLT/",
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:53:36.551850+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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},
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},
{
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],
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"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 76-100% 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": "2024-11-26T07:11:46.498661+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": "8fdb6d75-e22f-47a4-b42e-1a60d36517bc"
}