{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8504HJPW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8504HJPW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA_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 [IGVFDS8504HJPW](/measurement-sets/IGVFDS8504HJPW/) has in progress subobject auxiliary set [IGVFDS4645DCQC](/auxiliary-sets/IGVFDS4645DCQC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8504HJPW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0841TQDY](/in-vitro-systems/IGVFSM0841TQDY/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0841TQDY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8504HJPW](/measurement-sets/IGVFDS8504HJPW/) 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/IGVFDS8504HJPW/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4645DCQC](/auxiliary-sets/IGVFDS4645DCQC/) has sequence file(s) [IGVFFI8323HXWT](/sequence-files/IGVFFI8323HXWT/), [IGVFFI6647ECDQ](/sequence-files/IGVFFI6647ECDQ/), [IGVFFI5700TLJV](/sequence-files/IGVFFI5700TLJV/), [IGVFFI1697YVUG](/sequence-files/IGVFFI1697YVUG/), [IGVFFI1911BMFU](/sequence-files/IGVFFI1911BMFU/), [IGVFFI3724TACC](/sequence-files/IGVFFI3724TACC/), [IGVFFI6178DYAU](/sequence-files/IGVFFI6178DYAU/), [IGVFFI4302BDGU](/sequence-files/IGVFFI4302BDGU/), [IGVFFI0328TTPZ](/sequence-files/IGVFFI0328TTPZ/), [IGVFFI0818OYSO](/sequence-files/IGVFFI0818OYSO/), [IGVFFI1973MBPX](/sequence-files/IGVFFI1973MBPX/), [IGVFFI2232OBND](/sequence-files/IGVFFI2232OBND/), [IGVFFI6372RNHN](/sequence-files/IGVFFI6372RNHN/), [IGVFFI2399XUOF](/sequence-files/IGVFFI2399XUOF/), [IGVFFI6937SCLP](/sequence-files/IGVFFI6937SCLP/), [IGVFFI8225GSHC](/sequence-files/IGVFFI8225GSHC/), [IGVFFI2997QKPV](/sequence-files/IGVFFI2997QKPV/), [IGVFFI3960GRGF](/sequence-files/IGVFFI3960GRGF/), [IGVFFI0395YQWS](/sequence-files/IGVFFI0395YQWS/), [IGVFFI9129DQAA](/sequence-files/IGVFFI9129DQAA/), [IGVFFI8421JDKR](/sequence-files/IGVFFI8421JDKR/), [IGVFFI3120AKPC](/sequence-files/IGVFFI3120AKPC/), [IGVFFI1963JVTJ](/sequence-files/IGVFFI1963JVTJ/), [IGVFFI4922OUMR](/sequence-files/IGVFFI4922OUMR/), [IGVFFI7211NZTF](/sequence-files/IGVFFI7211NZTF/), [IGVFFI7652YXOS](/sequence-files/IGVFFI7652YXOS/), [IGVFFI4641NUDK](/sequence-files/IGVFFI4641NUDK/), [IGVFFI4941PTZU](/sequence-files/IGVFFI4941PTZU/), [IGVFFI2971HLBD](/sequence-files/IGVFFI2971HLBD/), [IGVFFI2565SEAF](/sequence-files/IGVFFI2565SEAF/), [IGVFFI0952NXHP](/sequence-files/IGVFFI0952NXHP/), [IGVFFI0955GZSP](/sequence-files/IGVFFI0955GZSP/), [IGVFFI6325ZJYX](/sequence-files/IGVFFI6325ZJYX/), [IGVFFI2537SZHL](/sequence-files/IGVFFI2537SZHL/), [IGVFFI9822TLTF](/sequence-files/IGVFFI9822TLTF/), [IGVFFI6851UEAY](/sequence-files/IGVFFI6851UEAY/), [IGVFFI6293JLMF](/sequence-files/IGVFFI6293JLMF/), [IGVFFI4165IHQU](/sequence-files/IGVFFI4165IHQU/), [IGVFFI0591WKKM](/sequence-files/IGVFFI0591WKKM/), [IGVFFI7627ESHC](/sequence-files/IGVFFI7627ESHC/), [IGVFFI0000LSBR](/sequence-files/IGVFFI0000LSBR/), [IGVFFI8413UPDY](/sequence-files/IGVFFI8413UPDY/), [IGVFFI0537RBSY](/sequence-files/IGVFFI0537RBSY/), [IGVFFI6184JBOY](/sequence-files/IGVFFI6184JBOY/), [IGVFFI2001HZEN](/sequence-files/IGVFFI2001HZEN/), [IGVFFI3420FNUL](/sequence-files/IGVFFI3420FNUL/), [IGVFFI5123FNRM](/sequence-files/IGVFFI5123FNRM/), [IGVFFI6845EQGG](/sequence-files/IGVFFI6845EQGG/) 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/IGVFDS4645DCQC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4645DCQC](/auxiliary-sets/IGVFDS4645DCQC/) has sequence file(s): [IGVFFI8323HXWT](/sequence-files/IGVFFI8323HXWT/), [IGVFFI6647ECDQ](/sequence-files/IGVFFI6647ECDQ/), [IGVFFI5700TLJV](/sequence-files/IGVFFI5700TLJV/), [IGVFFI1697YVUG](/sequence-files/IGVFFI1697YVUG/), [IGVFFI1911BMFU](/sequence-files/IGVFFI1911BMFU/), [IGVFFI3724TACC](/sequence-files/IGVFFI3724TACC/), [IGVFFI6178DYAU](/sequence-files/IGVFFI6178DYAU/), [IGVFFI4302BDGU](/sequence-files/IGVFFI4302BDGU/), [IGVFFI0328TTPZ](/sequence-files/IGVFFI0328TTPZ/), [IGVFFI0818OYSO](/sequence-files/IGVFFI0818OYSO/), [IGVFFI1973MBPX](/sequence-files/IGVFFI1973MBPX/), [IGVFFI2232OBND](/sequence-files/IGVFFI2232OBND/), [IGVFFI6372RNHN](/sequence-files/IGVFFI6372RNHN/), [IGVFFI2399XUOF](/sequence-files/IGVFFI2399XUOF/), [IGVFFI6937SCLP](/sequence-files/IGVFFI6937SCLP/), [IGVFFI8225GSHC](/sequence-files/IGVFFI8225GSHC/), [IGVFFI2997QKPV](/sequence-files/IGVFFI2997QKPV/), [IGVFFI3960GRGF](/sequence-files/IGVFFI3960GRGF/), [IGVFFI0395YQWS](/sequence-files/IGVFFI0395YQWS/), [IGVFFI9129DQAA](/sequence-files/IGVFFI9129DQAA/), [IGVFFI8421JDKR](/sequence-files/IGVFFI8421JDKR/), [IGVFFI3120AKPC](/sequence-files/IGVFFI3120AKPC/), [IGVFFI1963JVTJ](/sequence-files/IGVFFI1963JVTJ/), [IGVFFI4922OUMR](/sequence-files/IGVFFI4922OUMR/), [IGVFFI7211NZTF](/sequence-files/IGVFFI7211NZTF/), [IGVFFI7652YXOS](/sequence-files/IGVFFI7652YXOS/), [IGVFFI4641NUDK](/sequence-files/IGVFFI4641NUDK/), [IGVFFI4941PTZU](/sequence-files/IGVFFI4941PTZU/), [IGVFFI2971HLBD](/sequence-files/IGVFFI2971HLBD/), [IGVFFI2565SEAF](/sequence-files/IGVFFI2565SEAF/), [IGVFFI0952NXHP](/sequence-files/IGVFFI0952NXHP/), [IGVFFI0955GZSP](/sequence-files/IGVFFI0955GZSP/), [IGVFFI6325ZJYX](/sequence-files/IGVFFI6325ZJYX/), [IGVFFI2537SZHL](/sequence-files/IGVFFI2537SZHL/), [IGVFFI9822TLTF](/sequence-files/IGVFFI9822TLTF/), [IGVFFI6851UEAY](/sequence-files/IGVFFI6851UEAY/), [IGVFFI6293JLMF](/sequence-files/IGVFFI6293JLMF/), [IGVFFI4165IHQU](/sequence-files/IGVFFI4165IHQU/), [IGVFFI0591WKKM](/sequence-files/IGVFFI0591WKKM/), [IGVFFI7627ESHC](/sequence-files/IGVFFI7627ESHC/), [IGVFFI0000LSBR](/sequence-files/IGVFFI0000LSBR/), [IGVFFI8413UPDY](/sequence-files/IGVFFI8413UPDY/), [IGVFFI0537RBSY](/sequence-files/IGVFFI0537RBSY/), [IGVFFI6184JBOY](/sequence-files/IGVFFI6184JBOY/), [IGVFFI2001HZEN](/sequence-files/IGVFFI2001HZEN/), [IGVFFI3420FNUL](/sequence-files/IGVFFI3420FNUL/), [IGVFFI5123FNRM](/sequence-files/IGVFFI5123FNRM/), [IGVFFI6845EQGG](/sequence-files/IGVFFI6845EQGG/) 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/IGVFDS4645DCQC/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4645DCQC](/auxiliary-sets/IGVFDS4645DCQC/) 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/IGVFDS4645DCQC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4645DCQC/",
"accession": "IGVFDS4645DCQC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA_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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:08.596460+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/IGVFDS5031MNRR/"
],
"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": "2023-12-20T23:07:00.354494+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0841TQDY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0841TQDY",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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 0-25% 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": "2023-12-05T21:16:27.678449+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": "ef5a9a11-b681-40fb-acb0-401964b44f23"
}