{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6071XLAA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6071XLAA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-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 [IGVFDS6071XLAA](/measurement-sets/IGVFDS6071XLAA/) has in progress subobject auxiliary set [IGVFDS8184FIIP](/auxiliary-sets/IGVFDS8184FIIP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6071XLAA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5040QPRO](/in-vitro-systems/IGVFSM5040QPRO/) 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/IGVFSM5040QPRO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8184FIIP](/auxiliary-sets/IGVFDS8184FIIP/) has sequence file(s): [IGVFFI9443ZGZC](/sequence-files/IGVFFI9443ZGZC/), [IGVFFI0722GZHY](/sequence-files/IGVFFI0722GZHY/), [IGVFFI0224JDGO](/sequence-files/IGVFFI0224JDGO/), [IGVFFI7720EIBV](/sequence-files/IGVFFI7720EIBV/), [IGVFFI0008XSRO](/sequence-files/IGVFFI0008XSRO/), [IGVFFI3505PJZB](/sequence-files/IGVFFI3505PJZB/), [IGVFFI1626AMKM](/sequence-files/IGVFFI1626AMKM/), [IGVFFI8149LUHI](/sequence-files/IGVFFI8149LUHI/), [IGVFFI5352KGGP](/sequence-files/IGVFFI5352KGGP/), [IGVFFI8053JCMT](/sequence-files/IGVFFI8053JCMT/), [IGVFFI2648ZUFH](/sequence-files/IGVFFI2648ZUFH/), [IGVFFI7933VRZU](/sequence-files/IGVFFI7933VRZU/), [IGVFFI8956PDYX](/sequence-files/IGVFFI8956PDYX/), [IGVFFI7953WSZJ](/sequence-files/IGVFFI7953WSZJ/), [IGVFFI8041TBBD](/sequence-files/IGVFFI8041TBBD/), [IGVFFI9020CMHM](/sequence-files/IGVFFI9020CMHM/), [IGVFFI8801VOKH](/sequence-files/IGVFFI8801VOKH/), [IGVFFI6953LNTC](/sequence-files/IGVFFI6953LNTC/), [IGVFFI7873SGBU](/sequence-files/IGVFFI7873SGBU/), [IGVFFI7857WEFR](/sequence-files/IGVFFI7857WEFR/), [IGVFFI4381NFHJ](/sequence-files/IGVFFI4381NFHJ/), [IGVFFI5893PBZH](/sequence-files/IGVFFI5893PBZH/), [IGVFFI9726ROVJ](/sequence-files/IGVFFI9726ROVJ/), [IGVFFI8068QTGW](/sequence-files/IGVFFI8068QTGW/), [IGVFFI3696OSXV](/sequence-files/IGVFFI3696OSXV/), [IGVFFI1667HWTQ](/sequence-files/IGVFFI1667HWTQ/), [IGVFFI5323PYXG](/sequence-files/IGVFFI5323PYXG/), [IGVFFI8281TIQB](/sequence-files/IGVFFI8281TIQB/), [IGVFFI0637MWTB](/sequence-files/IGVFFI0637MWTB/), [IGVFFI0944LZTP](/sequence-files/IGVFFI0944LZTP/), [IGVFFI8642MAZK](/sequence-files/IGVFFI8642MAZK/), [IGVFFI3794GSRI](/sequence-files/IGVFFI3794GSRI/), [IGVFFI9395HRYY](/sequence-files/IGVFFI9395HRYY/), [IGVFFI6225DUUC](/sequence-files/IGVFFI6225DUUC/), [IGVFFI7808LBEB](/sequence-files/IGVFFI7808LBEB/), [IGVFFI8873HTNQ](/sequence-files/IGVFFI8873HTNQ/), [IGVFFI5718LWBF](/sequence-files/IGVFFI5718LWBF/), [IGVFFI8503BWOL](/sequence-files/IGVFFI8503BWOL/), [IGVFFI4322UEUW](/sequence-files/IGVFFI4322UEUW/), [IGVFFI0452OHDI](/sequence-files/IGVFFI0452OHDI/), [IGVFFI1510GDPS](/sequence-files/IGVFFI1510GDPS/), [IGVFFI3245EKTZ](/sequence-files/IGVFFI3245EKTZ/), [IGVFFI1090FUQZ](/sequence-files/IGVFFI1090FUQZ/), [IGVFFI1771ELYW](/sequence-files/IGVFFI1771ELYW/), [IGVFFI0756SUMN](/sequence-files/IGVFFI0756SUMN/), [IGVFFI9950AWEV](/sequence-files/IGVFFI9950AWEV/), [IGVFFI9214AQWH](/sequence-files/IGVFFI9214AQWH/), [IGVFFI5644FLWR](/sequence-files/IGVFFI5644FLWR/) 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/IGVFDS8184FIIP/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6071XLAA](/measurement-sets/IGVFDS6071XLAA/) 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/IGVFDS6071XLAA/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8184FIIP](/auxiliary-sets/IGVFDS8184FIIP/) has sequence file(s) [IGVFFI9443ZGZC](/sequence-files/IGVFFI9443ZGZC/), [IGVFFI0722GZHY](/sequence-files/IGVFFI0722GZHY/), [IGVFFI0224JDGO](/sequence-files/IGVFFI0224JDGO/), [IGVFFI7720EIBV](/sequence-files/IGVFFI7720EIBV/), [IGVFFI0008XSRO](/sequence-files/IGVFFI0008XSRO/), [IGVFFI3505PJZB](/sequence-files/IGVFFI3505PJZB/), [IGVFFI1626AMKM](/sequence-files/IGVFFI1626AMKM/), [IGVFFI8149LUHI](/sequence-files/IGVFFI8149LUHI/), [IGVFFI5352KGGP](/sequence-files/IGVFFI5352KGGP/), [IGVFFI8053JCMT](/sequence-files/IGVFFI8053JCMT/), [IGVFFI2648ZUFH](/sequence-files/IGVFFI2648ZUFH/), [IGVFFI7933VRZU](/sequence-files/IGVFFI7933VRZU/), [IGVFFI8956PDYX](/sequence-files/IGVFFI8956PDYX/), [IGVFFI7953WSZJ](/sequence-files/IGVFFI7953WSZJ/), [IGVFFI8041TBBD](/sequence-files/IGVFFI8041TBBD/), [IGVFFI9020CMHM](/sequence-files/IGVFFI9020CMHM/), [IGVFFI8801VOKH](/sequence-files/IGVFFI8801VOKH/), [IGVFFI6953LNTC](/sequence-files/IGVFFI6953LNTC/), [IGVFFI7873SGBU](/sequence-files/IGVFFI7873SGBU/), [IGVFFI7857WEFR](/sequence-files/IGVFFI7857WEFR/), [IGVFFI4381NFHJ](/sequence-files/IGVFFI4381NFHJ/), [IGVFFI5893PBZH](/sequence-files/IGVFFI5893PBZH/), [IGVFFI9726ROVJ](/sequence-files/IGVFFI9726ROVJ/), [IGVFFI8068QTGW](/sequence-files/IGVFFI8068QTGW/), [IGVFFI3696OSXV](/sequence-files/IGVFFI3696OSXV/), [IGVFFI1667HWTQ](/sequence-files/IGVFFI1667HWTQ/), [IGVFFI5323PYXG](/sequence-files/IGVFFI5323PYXG/), [IGVFFI8281TIQB](/sequence-files/IGVFFI8281TIQB/), [IGVFFI0637MWTB](/sequence-files/IGVFFI0637MWTB/), [IGVFFI0944LZTP](/sequence-files/IGVFFI0944LZTP/), [IGVFFI8642MAZK](/sequence-files/IGVFFI8642MAZK/), [IGVFFI3794GSRI](/sequence-files/IGVFFI3794GSRI/), [IGVFFI9395HRYY](/sequence-files/IGVFFI9395HRYY/), [IGVFFI6225DUUC](/sequence-files/IGVFFI6225DUUC/), [IGVFFI7808LBEB](/sequence-files/IGVFFI7808LBEB/), [IGVFFI8873HTNQ](/sequence-files/IGVFFI8873HTNQ/), [IGVFFI5718LWBF](/sequence-files/IGVFFI5718LWBF/), [IGVFFI8503BWOL](/sequence-files/IGVFFI8503BWOL/), [IGVFFI4322UEUW](/sequence-files/IGVFFI4322UEUW/), [IGVFFI0452OHDI](/sequence-files/IGVFFI0452OHDI/), [IGVFFI1510GDPS](/sequence-files/IGVFFI1510GDPS/), [IGVFFI3245EKTZ](/sequence-files/IGVFFI3245EKTZ/), [IGVFFI1090FUQZ](/sequence-files/IGVFFI1090FUQZ/), [IGVFFI1771ELYW](/sequence-files/IGVFFI1771ELYW/), [IGVFFI0756SUMN](/sequence-files/IGVFFI0756SUMN/), [IGVFFI9950AWEV](/sequence-files/IGVFFI9950AWEV/), [IGVFFI9214AQWH](/sequence-files/IGVFFI9214AQWH/), [IGVFFI5644FLWR](/sequence-files/IGVFFI5644FLWR/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8184FIIP/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8184FIIP](/auxiliary-sets/IGVFDS8184FIIP/) 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/IGVFDS8184FIIP/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8184FIIP/",
"accession": "IGVFDS8184FIIP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-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": "2023-11-30T22:48:57.651032+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": "2023-12-20T23:05:48.305153+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5040QPRO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5040QPRO",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-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": "20",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T20:14:19.621860+00:00",
"summary": "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": "eeec16fe-273a-44b0-b8b4-ab4d1ca14101"
}