{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5341DFHM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5341DFHM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinB_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 [IGVFDS5341DFHM](/measurement-sets/IGVFDS5341DFHM/) has in progress subobject auxiliary set [IGVFDS9278ESDK](/auxiliary-sets/IGVFDS9278ESDK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5341DFHM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3794OZOG](/in-vitro-systems/IGVFSM3794OZOG/) 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/IGVFSM3794OZOG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5341DFHM](/measurement-sets/IGVFDS5341DFHM/) 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/IGVFDS5341DFHM/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9278ESDK](/auxiliary-sets/IGVFDS9278ESDK/) has sequence file(s) [IGVFFI5675NIUY](/sequence-files/IGVFFI5675NIUY/), [IGVFFI1090NFMB](/sequence-files/IGVFFI1090NFMB/), [IGVFFI3703EBTL](/sequence-files/IGVFFI3703EBTL/), [IGVFFI4309DAPG](/sequence-files/IGVFFI4309DAPG/), [IGVFFI5608LBWW](/sequence-files/IGVFFI5608LBWW/), [IGVFFI3527ETOI](/sequence-files/IGVFFI3527ETOI/), [IGVFFI3217BFXA](/sequence-files/IGVFFI3217BFXA/), [IGVFFI6414PJUV](/sequence-files/IGVFFI6414PJUV/), [IGVFFI1341MLBR](/sequence-files/IGVFFI1341MLBR/), [IGVFFI6409ZHPQ](/sequence-files/IGVFFI6409ZHPQ/), [IGVFFI6084BLGQ](/sequence-files/IGVFFI6084BLGQ/), [IGVFFI4314REOB](/sequence-files/IGVFFI4314REOB/), [IGVFFI1205AZHU](/sequence-files/IGVFFI1205AZHU/), [IGVFFI0489BVLU](/sequence-files/IGVFFI0489BVLU/), [IGVFFI2951KQUX](/sequence-files/IGVFFI2951KQUX/), [IGVFFI1582JZJA](/sequence-files/IGVFFI1582JZJA/), [IGVFFI1656UOEF](/sequence-files/IGVFFI1656UOEF/), [IGVFFI5386FFSM](/sequence-files/IGVFFI5386FFSM/), [IGVFFI2654TOIY](/sequence-files/IGVFFI2654TOIY/), [IGVFFI5622HXWF](/sequence-files/IGVFFI5622HXWF/), [IGVFFI6020TZCV](/sequence-files/IGVFFI6020TZCV/), [IGVFFI8497HABY](/sequence-files/IGVFFI8497HABY/), [IGVFFI4619NIRP](/sequence-files/IGVFFI4619NIRP/), [IGVFFI0908HNBD](/sequence-files/IGVFFI0908HNBD/), [IGVFFI7892JUHM](/sequence-files/IGVFFI7892JUHM/), [IGVFFI5751TCVS](/sequence-files/IGVFFI5751TCVS/), [IGVFFI4689NQNE](/sequence-files/IGVFFI4689NQNE/), [IGVFFI3678MOEY](/sequence-files/IGVFFI3678MOEY/), [IGVFFI0332BJPV](/sequence-files/IGVFFI0332BJPV/), [IGVFFI8367FUZD](/sequence-files/IGVFFI8367FUZD/), [IGVFFI2995ZRFH](/sequence-files/IGVFFI2995ZRFH/), [IGVFFI0226HZOX](/sequence-files/IGVFFI0226HZOX/), [IGVFFI8967BWYO](/sequence-files/IGVFFI8967BWYO/), [IGVFFI5821YZCD](/sequence-files/IGVFFI5821YZCD/), [IGVFFI9504WNOR](/sequence-files/IGVFFI9504WNOR/), [IGVFFI1673HCRO](/sequence-files/IGVFFI1673HCRO/), [IGVFFI7364VDTT](/sequence-files/IGVFFI7364VDTT/), [IGVFFI6948SGDC](/sequence-files/IGVFFI6948SGDC/), [IGVFFI4903LWUG](/sequence-files/IGVFFI4903LWUG/), [IGVFFI3610MGBE](/sequence-files/IGVFFI3610MGBE/), [IGVFFI2355CGWD](/sequence-files/IGVFFI2355CGWD/), [IGVFFI9856HIMF](/sequence-files/IGVFFI9856HIMF/), [IGVFFI8325DPGJ](/sequence-files/IGVFFI8325DPGJ/), [IGVFFI2275NISI](/sequence-files/IGVFFI2275NISI/), [IGVFFI4980UAMK](/sequence-files/IGVFFI4980UAMK/), [IGVFFI0547HKKZ](/sequence-files/IGVFFI0547HKKZ/), [IGVFFI1555KDXH](/sequence-files/IGVFFI1555KDXH/), [IGVFFI1154KTEF](/sequence-files/IGVFFI1154KTEF/) 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/IGVFDS9278ESDK/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9278ESDK](/auxiliary-sets/IGVFDS9278ESDK/) has sequence file(s): [IGVFFI5675NIUY](/sequence-files/IGVFFI5675NIUY/), [IGVFFI1090NFMB](/sequence-files/IGVFFI1090NFMB/), [IGVFFI3703EBTL](/sequence-files/IGVFFI3703EBTL/), [IGVFFI4309DAPG](/sequence-files/IGVFFI4309DAPG/), [IGVFFI5608LBWW](/sequence-files/IGVFFI5608LBWW/), [IGVFFI3527ETOI](/sequence-files/IGVFFI3527ETOI/), [IGVFFI3217BFXA](/sequence-files/IGVFFI3217BFXA/), [IGVFFI6414PJUV](/sequence-files/IGVFFI6414PJUV/), [IGVFFI1341MLBR](/sequence-files/IGVFFI1341MLBR/), [IGVFFI6409ZHPQ](/sequence-files/IGVFFI6409ZHPQ/), [IGVFFI6084BLGQ](/sequence-files/IGVFFI6084BLGQ/), [IGVFFI4314REOB](/sequence-files/IGVFFI4314REOB/), [IGVFFI1205AZHU](/sequence-files/IGVFFI1205AZHU/), [IGVFFI0489BVLU](/sequence-files/IGVFFI0489BVLU/), [IGVFFI2951KQUX](/sequence-files/IGVFFI2951KQUX/), [IGVFFI1582JZJA](/sequence-files/IGVFFI1582JZJA/), [IGVFFI1656UOEF](/sequence-files/IGVFFI1656UOEF/), [IGVFFI5386FFSM](/sequence-files/IGVFFI5386FFSM/), [IGVFFI2654TOIY](/sequence-files/IGVFFI2654TOIY/), [IGVFFI5622HXWF](/sequence-files/IGVFFI5622HXWF/), [IGVFFI6020TZCV](/sequence-files/IGVFFI6020TZCV/), [IGVFFI8497HABY](/sequence-files/IGVFFI8497HABY/), [IGVFFI4619NIRP](/sequence-files/IGVFFI4619NIRP/), [IGVFFI0908HNBD](/sequence-files/IGVFFI0908HNBD/), [IGVFFI7892JUHM](/sequence-files/IGVFFI7892JUHM/), [IGVFFI5751TCVS](/sequence-files/IGVFFI5751TCVS/), [IGVFFI4689NQNE](/sequence-files/IGVFFI4689NQNE/), [IGVFFI3678MOEY](/sequence-files/IGVFFI3678MOEY/), [IGVFFI0332BJPV](/sequence-files/IGVFFI0332BJPV/), [IGVFFI8367FUZD](/sequence-files/IGVFFI8367FUZD/), [IGVFFI2995ZRFH](/sequence-files/IGVFFI2995ZRFH/), [IGVFFI0226HZOX](/sequence-files/IGVFFI0226HZOX/), [IGVFFI8967BWYO](/sequence-files/IGVFFI8967BWYO/), [IGVFFI5821YZCD](/sequence-files/IGVFFI5821YZCD/), [IGVFFI9504WNOR](/sequence-files/IGVFFI9504WNOR/), [IGVFFI1673HCRO](/sequence-files/IGVFFI1673HCRO/), [IGVFFI7364VDTT](/sequence-files/IGVFFI7364VDTT/), [IGVFFI6948SGDC](/sequence-files/IGVFFI6948SGDC/), [IGVFFI4903LWUG](/sequence-files/IGVFFI4903LWUG/), [IGVFFI3610MGBE](/sequence-files/IGVFFI3610MGBE/), [IGVFFI2355CGWD](/sequence-files/IGVFFI2355CGWD/), [IGVFFI9856HIMF](/sequence-files/IGVFFI9856HIMF/), [IGVFFI8325DPGJ](/sequence-files/IGVFFI8325DPGJ/), [IGVFFI2275NISI](/sequence-files/IGVFFI2275NISI/), [IGVFFI4980UAMK](/sequence-files/IGVFFI4980UAMK/), [IGVFFI0547HKKZ](/sequence-files/IGVFFI0547HKKZ/), [IGVFFI1555KDXH](/sequence-files/IGVFFI1555KDXH/), [IGVFFI1154KTEF](/sequence-files/IGVFFI1154KTEF/) 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/IGVFDS9278ESDK/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9278ESDK](/auxiliary-sets/IGVFDS9278ESDK/) 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/IGVFDS9278ESDK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9278ESDK/",
"accession": "IGVFDS9278ESDK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinB_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": "2023-11-30T22:48:59.649835+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": "2023-12-20T23:05:18.727434+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3794OZOG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3794OZOG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinB"
],
"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 26-50% 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": "2023-12-05T20:23:06.062286+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": "948acf22-b623-479d-bd7a-f1286250dcc4"
}