{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1783OBDQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1783OBDQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-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 in vitro system [IGVFSM3986RDKP](/in-vitro-systems/IGVFSM3986RDKP/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3986RDKP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1783OBDQ](/measurement-sets/IGVFDS1783OBDQ/) has in progress subobject auxiliary set [IGVFDS0226MNQK](/auxiliary-sets/IGVFDS0226MNQK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1783OBDQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0226MNQK](/auxiliary-sets/IGVFDS0226MNQK/) has sequence file(s): [IGVFFI7868ERJC](/sequence-files/IGVFFI7868ERJC/), [IGVFFI6570GECU](/sequence-files/IGVFFI6570GECU/), [IGVFFI1084WWWI](/sequence-files/IGVFFI1084WWWI/), [IGVFFI4328ILVD](/sequence-files/IGVFFI4328ILVD/), [IGVFFI8365JVYQ](/sequence-files/IGVFFI8365JVYQ/), [IGVFFI0700KBYN](/sequence-files/IGVFFI0700KBYN/), [IGVFFI4490WQLD](/sequence-files/IGVFFI4490WQLD/), [IGVFFI7780BWMD](/sequence-files/IGVFFI7780BWMD/), [IGVFFI3918IXHP](/sequence-files/IGVFFI3918IXHP/), [IGVFFI3401PMYQ](/sequence-files/IGVFFI3401PMYQ/), [IGVFFI2372UNMC](/sequence-files/IGVFFI2372UNMC/), [IGVFFI4906AQJD](/sequence-files/IGVFFI4906AQJD/), [IGVFFI1544GAUM](/sequence-files/IGVFFI1544GAUM/), [IGVFFI2787RXXU](/sequence-files/IGVFFI2787RXXU/), [IGVFFI4323LSBH](/sequence-files/IGVFFI4323LSBH/), [IGVFFI8098YOGQ](/sequence-files/IGVFFI8098YOGQ/), [IGVFFI2164MEMX](/sequence-files/IGVFFI2164MEMX/), [IGVFFI5454APPU](/sequence-files/IGVFFI5454APPU/), [IGVFFI1587HKAU](/sequence-files/IGVFFI1587HKAU/), [IGVFFI6256RSXK](/sequence-files/IGVFFI6256RSXK/), [IGVFFI8157LOFU](/sequence-files/IGVFFI8157LOFU/), [IGVFFI8234BGBN](/sequence-files/IGVFFI8234BGBN/), [IGVFFI9353KKSR](/sequence-files/IGVFFI9353KKSR/), [IGVFFI3894JBGH](/sequence-files/IGVFFI3894JBGH/), [IGVFFI3196UNZG](/sequence-files/IGVFFI3196UNZG/), [IGVFFI1392DWWT](/sequence-files/IGVFFI1392DWWT/), [IGVFFI2292PYPW](/sequence-files/IGVFFI2292PYPW/), [IGVFFI5384OHPY](/sequence-files/IGVFFI5384OHPY/), [IGVFFI6644FHZZ](/sequence-files/IGVFFI6644FHZZ/), [IGVFFI3640VZZP](/sequence-files/IGVFFI3640VZZP/), [IGVFFI8834HKHY](/sequence-files/IGVFFI8834HKHY/), [IGVFFI2821MKFB](/sequence-files/IGVFFI2821MKFB/), [IGVFFI5634QVAU](/sequence-files/IGVFFI5634QVAU/), [IGVFFI9981FXPK](/sequence-files/IGVFFI9981FXPK/), [IGVFFI4266WRZV](/sequence-files/IGVFFI4266WRZV/), [IGVFFI9489NFMA](/sequence-files/IGVFFI9489NFMA/), [IGVFFI5273XXMZ](/sequence-files/IGVFFI5273XXMZ/), [IGVFFI9697VTJX](/sequence-files/IGVFFI9697VTJX/), [IGVFFI7553WZJO](/sequence-files/IGVFFI7553WZJO/), [IGVFFI1419EGJU](/sequence-files/IGVFFI1419EGJU/), [IGVFFI4963FEUF](/sequence-files/IGVFFI4963FEUF/), [IGVFFI3445JMTA](/sequence-files/IGVFFI3445JMTA/), [IGVFFI8394CAAJ](/sequence-files/IGVFFI8394CAAJ/), [IGVFFI6070NNFA](/sequence-files/IGVFFI6070NNFA/), [IGVFFI1292KVQH](/sequence-files/IGVFFI1292KVQH/), [IGVFFI5865IQFR](/sequence-files/IGVFFI5865IQFR/), [IGVFFI1468BKHX](/sequence-files/IGVFFI1468BKHX/), [IGVFFI5966HRBE](/sequence-files/IGVFFI5966HRBE/) 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/IGVFDS0226MNQK/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1783OBDQ](/measurement-sets/IGVFDS1783OBDQ/) 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/IGVFDS1783OBDQ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0226MNQK](/auxiliary-sets/IGVFDS0226MNQK/) has sequence file(s) [IGVFFI7868ERJC](/sequence-files/IGVFFI7868ERJC/), [IGVFFI6570GECU](/sequence-files/IGVFFI6570GECU/), [IGVFFI1084WWWI](/sequence-files/IGVFFI1084WWWI/), [IGVFFI4328ILVD](/sequence-files/IGVFFI4328ILVD/), [IGVFFI8365JVYQ](/sequence-files/IGVFFI8365JVYQ/), [IGVFFI0700KBYN](/sequence-files/IGVFFI0700KBYN/), [IGVFFI4490WQLD](/sequence-files/IGVFFI4490WQLD/), [IGVFFI7780BWMD](/sequence-files/IGVFFI7780BWMD/), [IGVFFI3918IXHP](/sequence-files/IGVFFI3918IXHP/), [IGVFFI3401PMYQ](/sequence-files/IGVFFI3401PMYQ/), [IGVFFI2372UNMC](/sequence-files/IGVFFI2372UNMC/), [IGVFFI4906AQJD](/sequence-files/IGVFFI4906AQJD/), [IGVFFI1544GAUM](/sequence-files/IGVFFI1544GAUM/), [IGVFFI2787RXXU](/sequence-files/IGVFFI2787RXXU/), [IGVFFI4323LSBH](/sequence-files/IGVFFI4323LSBH/), [IGVFFI8098YOGQ](/sequence-files/IGVFFI8098YOGQ/), [IGVFFI2164MEMX](/sequence-files/IGVFFI2164MEMX/), [IGVFFI5454APPU](/sequence-files/IGVFFI5454APPU/), [IGVFFI1587HKAU](/sequence-files/IGVFFI1587HKAU/), [IGVFFI6256RSXK](/sequence-files/IGVFFI6256RSXK/), [IGVFFI8157LOFU](/sequence-files/IGVFFI8157LOFU/), [IGVFFI8234BGBN](/sequence-files/IGVFFI8234BGBN/), [IGVFFI9353KKSR](/sequence-files/IGVFFI9353KKSR/), [IGVFFI3894JBGH](/sequence-files/IGVFFI3894JBGH/), [IGVFFI3196UNZG](/sequence-files/IGVFFI3196UNZG/), [IGVFFI1392DWWT](/sequence-files/IGVFFI1392DWWT/), [IGVFFI2292PYPW](/sequence-files/IGVFFI2292PYPW/), [IGVFFI5384OHPY](/sequence-files/IGVFFI5384OHPY/), [IGVFFI6644FHZZ](/sequence-files/IGVFFI6644FHZZ/), [IGVFFI3640VZZP](/sequence-files/IGVFFI3640VZZP/), [IGVFFI8834HKHY](/sequence-files/IGVFFI8834HKHY/), [IGVFFI2821MKFB](/sequence-files/IGVFFI2821MKFB/), [IGVFFI5634QVAU](/sequence-files/IGVFFI5634QVAU/), [IGVFFI9981FXPK](/sequence-files/IGVFFI9981FXPK/), [IGVFFI4266WRZV](/sequence-files/IGVFFI4266WRZV/), [IGVFFI9489NFMA](/sequence-files/IGVFFI9489NFMA/), [IGVFFI5273XXMZ](/sequence-files/IGVFFI5273XXMZ/), [IGVFFI9697VTJX](/sequence-files/IGVFFI9697VTJX/), [IGVFFI7553WZJO](/sequence-files/IGVFFI7553WZJO/), [IGVFFI1419EGJU](/sequence-files/IGVFFI1419EGJU/), [IGVFFI4963FEUF](/sequence-files/IGVFFI4963FEUF/), [IGVFFI3445JMTA](/sequence-files/IGVFFI3445JMTA/), [IGVFFI8394CAAJ](/sequence-files/IGVFFI8394CAAJ/), [IGVFFI6070NNFA](/sequence-files/IGVFFI6070NNFA/), [IGVFFI1292KVQH](/sequence-files/IGVFFI1292KVQH/), [IGVFFI5865IQFR](/sequence-files/IGVFFI5865IQFR/), [IGVFFI1468BKHX](/sequence-files/IGVFFI1468BKHX/), [IGVFFI5966HRBE](/sequence-files/IGVFFI5966HRBE/) 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/IGVFDS0226MNQK/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0226MNQK](/auxiliary-sets/IGVFDS0226MNQK/) 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/IGVFDS0226MNQK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0226MNQK/",
"accession": "IGVFDS0226MNQK",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:05.260621+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/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:32.249038+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3986RDKP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3986RDKP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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 a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T22:36:50.334509+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": "306ad3e9-1974-44cb-9f19-f9aeb3702478"
}