{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0621TDYK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0621TDYK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-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 [IGVFSM3264VOCP](/in-vitro-systems/IGVFSM3264VOCP/) 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/IGVFSM3264VOCP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0621TDYK](/measurement-sets/IGVFDS0621TDYK/) has in progress subobject auxiliary set [IGVFDS7780VSEK](/auxiliary-sets/IGVFDS7780VSEK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0621TDYK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7780VSEK](/auxiliary-sets/IGVFDS7780VSEK/) has sequence file(s) [IGVFFI3608DOEV](/sequence-files/IGVFFI3608DOEV/), [IGVFFI0394WTJE](/sequence-files/IGVFFI0394WTJE/), [IGVFFI6298IPGY](/sequence-files/IGVFFI6298IPGY/), [IGVFFI3740ZFUI](/sequence-files/IGVFFI3740ZFUI/), [IGVFFI0346XIJH](/sequence-files/IGVFFI0346XIJH/), [IGVFFI3854NDPL](/sequence-files/IGVFFI3854NDPL/), [IGVFFI1422MCHI](/sequence-files/IGVFFI1422MCHI/), [IGVFFI5930AYLY](/sequence-files/IGVFFI5930AYLY/), [IGVFFI9645BTMH](/sequence-files/IGVFFI9645BTMH/), [IGVFFI4437FPJT](/sequence-files/IGVFFI4437FPJT/), [IGVFFI9061JNFF](/sequence-files/IGVFFI9061JNFF/), [IGVFFI0372VOOV](/sequence-files/IGVFFI0372VOOV/), [IGVFFI4605LBMF](/sequence-files/IGVFFI4605LBMF/), [IGVFFI7296FPVL](/sequence-files/IGVFFI7296FPVL/), [IGVFFI3411JNEQ](/sequence-files/IGVFFI3411JNEQ/), [IGVFFI8099IKLL](/sequence-files/IGVFFI8099IKLL/), [IGVFFI6162CLIQ](/sequence-files/IGVFFI6162CLIQ/), [IGVFFI9549DAOG](/sequence-files/IGVFFI9549DAOG/), [IGVFFI4970KHYZ](/sequence-files/IGVFFI4970KHYZ/), [IGVFFI9651YFGG](/sequence-files/IGVFFI9651YFGG/), [IGVFFI0698GTIH](/sequence-files/IGVFFI0698GTIH/), [IGVFFI1734SCAD](/sequence-files/IGVFFI1734SCAD/), [IGVFFI0481USKB](/sequence-files/IGVFFI0481USKB/), [IGVFFI4021ZFJW](/sequence-files/IGVFFI4021ZFJW/), [IGVFFI9873JKPN](/sequence-files/IGVFFI9873JKPN/), [IGVFFI9890JLQX](/sequence-files/IGVFFI9890JLQX/), [IGVFFI4499DMSW](/sequence-files/IGVFFI4499DMSW/), [IGVFFI2729JUTK](/sequence-files/IGVFFI2729JUTK/), [IGVFFI4011YQLR](/sequence-files/IGVFFI4011YQLR/), [IGVFFI7822LUBQ](/sequence-files/IGVFFI7822LUBQ/), [IGVFFI8524OXGK](/sequence-files/IGVFFI8524OXGK/), [IGVFFI0840TFUH](/sequence-files/IGVFFI0840TFUH/), [IGVFFI2527DBCS](/sequence-files/IGVFFI2527DBCS/), [IGVFFI8655NZXM](/sequence-files/IGVFFI8655NZXM/), [IGVFFI2749RFAT](/sequence-files/IGVFFI2749RFAT/), [IGVFFI8505ZMCR](/sequence-files/IGVFFI8505ZMCR/), [IGVFFI9904KPHO](/sequence-files/IGVFFI9904KPHO/), [IGVFFI9187WVNL](/sequence-files/IGVFFI9187WVNL/), [IGVFFI7346QUFM](/sequence-files/IGVFFI7346QUFM/), [IGVFFI7017IDNO](/sequence-files/IGVFFI7017IDNO/), [IGVFFI9947DWOB](/sequence-files/IGVFFI9947DWOB/), [IGVFFI8672FJGM](/sequence-files/IGVFFI8672FJGM/), [IGVFFI9227GJAS](/sequence-files/IGVFFI9227GJAS/), [IGVFFI3241JEHX](/sequence-files/IGVFFI3241JEHX/), [IGVFFI2164HHSW](/sequence-files/IGVFFI2164HHSW/), [IGVFFI3268NBNX](/sequence-files/IGVFFI3268NBNX/), [IGVFFI6643KWMV](/sequence-files/IGVFFI6643KWMV/), [IGVFFI3111RZMZ](/sequence-files/IGVFFI3111RZMZ/) 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/IGVFDS7780VSEK/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7780VSEK](/auxiliary-sets/IGVFDS7780VSEK/) has sequence file(s): [IGVFFI3608DOEV](/sequence-files/IGVFFI3608DOEV/), [IGVFFI0394WTJE](/sequence-files/IGVFFI0394WTJE/), [IGVFFI6298IPGY](/sequence-files/IGVFFI6298IPGY/), [IGVFFI3740ZFUI](/sequence-files/IGVFFI3740ZFUI/), [IGVFFI0346XIJH](/sequence-files/IGVFFI0346XIJH/), [IGVFFI3854NDPL](/sequence-files/IGVFFI3854NDPL/), [IGVFFI1422MCHI](/sequence-files/IGVFFI1422MCHI/), [IGVFFI5930AYLY](/sequence-files/IGVFFI5930AYLY/), [IGVFFI9645BTMH](/sequence-files/IGVFFI9645BTMH/), [IGVFFI4437FPJT](/sequence-files/IGVFFI4437FPJT/), [IGVFFI9061JNFF](/sequence-files/IGVFFI9061JNFF/), [IGVFFI0372VOOV](/sequence-files/IGVFFI0372VOOV/), [IGVFFI4605LBMF](/sequence-files/IGVFFI4605LBMF/), [IGVFFI7296FPVL](/sequence-files/IGVFFI7296FPVL/), [IGVFFI3411JNEQ](/sequence-files/IGVFFI3411JNEQ/), [IGVFFI8099IKLL](/sequence-files/IGVFFI8099IKLL/), [IGVFFI6162CLIQ](/sequence-files/IGVFFI6162CLIQ/), [IGVFFI9549DAOG](/sequence-files/IGVFFI9549DAOG/), [IGVFFI4970KHYZ](/sequence-files/IGVFFI4970KHYZ/), [IGVFFI9651YFGG](/sequence-files/IGVFFI9651YFGG/), [IGVFFI0698GTIH](/sequence-files/IGVFFI0698GTIH/), [IGVFFI1734SCAD](/sequence-files/IGVFFI1734SCAD/), [IGVFFI0481USKB](/sequence-files/IGVFFI0481USKB/), [IGVFFI4021ZFJW](/sequence-files/IGVFFI4021ZFJW/), [IGVFFI9873JKPN](/sequence-files/IGVFFI9873JKPN/), [IGVFFI9890JLQX](/sequence-files/IGVFFI9890JLQX/), [IGVFFI4499DMSW](/sequence-files/IGVFFI4499DMSW/), [IGVFFI2729JUTK](/sequence-files/IGVFFI2729JUTK/), [IGVFFI4011YQLR](/sequence-files/IGVFFI4011YQLR/), [IGVFFI7822LUBQ](/sequence-files/IGVFFI7822LUBQ/), [IGVFFI8524OXGK](/sequence-files/IGVFFI8524OXGK/), [IGVFFI0840TFUH](/sequence-files/IGVFFI0840TFUH/), [IGVFFI2527DBCS](/sequence-files/IGVFFI2527DBCS/), [IGVFFI8655NZXM](/sequence-files/IGVFFI8655NZXM/), [IGVFFI2749RFAT](/sequence-files/IGVFFI2749RFAT/), [IGVFFI8505ZMCR](/sequence-files/IGVFFI8505ZMCR/), [IGVFFI9904KPHO](/sequence-files/IGVFFI9904KPHO/), [IGVFFI9187WVNL](/sequence-files/IGVFFI9187WVNL/), [IGVFFI7346QUFM](/sequence-files/IGVFFI7346QUFM/), [IGVFFI7017IDNO](/sequence-files/IGVFFI7017IDNO/), [IGVFFI9947DWOB](/sequence-files/IGVFFI9947DWOB/), [IGVFFI8672FJGM](/sequence-files/IGVFFI8672FJGM/), [IGVFFI9227GJAS](/sequence-files/IGVFFI9227GJAS/), [IGVFFI3241JEHX](/sequence-files/IGVFFI3241JEHX/), [IGVFFI2164HHSW](/sequence-files/IGVFFI2164HHSW/), [IGVFFI3268NBNX](/sequence-files/IGVFFI3268NBNX/), [IGVFFI6643KWMV](/sequence-files/IGVFFI6643KWMV/), [IGVFFI3111RZMZ](/sequence-files/IGVFFI3111RZMZ/) 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/IGVFDS7780VSEK/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0621TDYK](/measurement-sets/IGVFDS0621TDYK/) 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/IGVFDS0621TDYK/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7780VSEK](/auxiliary-sets/IGVFDS7780VSEK/) 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_for",
"path": "/auxiliary-sets/IGVFDS7780VSEK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7780VSEK/",
"accession": "IGVFDS7780VSEK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:06.173103+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",
"files": [],
"input_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": "2023-12-20T23:05:14.269297+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3264VOCP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3264VOCP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC"
],
"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 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected 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": "2023-12-05T21:01:33.351967+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": "04821987-51be-4e95-b227-b89c921654a3"
}