{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1327XCCU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1327XCCU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-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 [IGVFDS1327XCCU](/measurement-sets/IGVFDS1327XCCU/) has in progress subobject auxiliary set [IGVFDS6359FZHI](/auxiliary-sets/IGVFDS6359FZHI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1327XCCU/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5844KEUJ](/in-vitro-systems/IGVFSM5844KEUJ/) 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/IGVFSM5844KEUJ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1327XCCU](/measurement-sets/IGVFDS1327XCCU/) 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/IGVFDS1327XCCU/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6359FZHI](/auxiliary-sets/IGVFDS6359FZHI/) has sequence file(s): [IGVFFI3043STQW](/sequence-files/IGVFFI3043STQW/), [IGVFFI6997XITK](/sequence-files/IGVFFI6997XITK/), [IGVFFI5278LQAY](/sequence-files/IGVFFI5278LQAY/), [IGVFFI5180CXKH](/sequence-files/IGVFFI5180CXKH/), [IGVFFI8745VLNT](/sequence-files/IGVFFI8745VLNT/), [IGVFFI3066LWHM](/sequence-files/IGVFFI3066LWHM/), [IGVFFI9429JMOJ](/sequence-files/IGVFFI9429JMOJ/), [IGVFFI5607TJVZ](/sequence-files/IGVFFI5607TJVZ/), [IGVFFI9742SYME](/sequence-files/IGVFFI9742SYME/), [IGVFFI7338DWWK](/sequence-files/IGVFFI7338DWWK/), [IGVFFI6399PGJQ](/sequence-files/IGVFFI6399PGJQ/), [IGVFFI6401MICT](/sequence-files/IGVFFI6401MICT/), [IGVFFI4807AAZI](/sequence-files/IGVFFI4807AAZI/), [IGVFFI7350UQLW](/sequence-files/IGVFFI7350UQLW/), [IGVFFI6213BYUY](/sequence-files/IGVFFI6213BYUY/), [IGVFFI9207IDMM](/sequence-files/IGVFFI9207IDMM/), [IGVFFI7121SZJD](/sequence-files/IGVFFI7121SZJD/), [IGVFFI7747ROLT](/sequence-files/IGVFFI7747ROLT/), [IGVFFI3609QXCK](/sequence-files/IGVFFI3609QXCK/), [IGVFFI0938WPJU](/sequence-files/IGVFFI0938WPJU/), [IGVFFI5747LSNL](/sequence-files/IGVFFI5747LSNL/), [IGVFFI0018FVXE](/sequence-files/IGVFFI0018FVXE/), [IGVFFI6612TAEI](/sequence-files/IGVFFI6612TAEI/), [IGVFFI0174HPHA](/sequence-files/IGVFFI0174HPHA/), [IGVFFI5168KASR](/sequence-files/IGVFFI5168KASR/), [IGVFFI0555LQIR](/sequence-files/IGVFFI0555LQIR/), [IGVFFI1078IQWD](/sequence-files/IGVFFI1078IQWD/), [IGVFFI2217TFSA](/sequence-files/IGVFFI2217TFSA/), [IGVFFI0071ZIGG](/sequence-files/IGVFFI0071ZIGG/), [IGVFFI2303HBSE](/sequence-files/IGVFFI2303HBSE/), [IGVFFI0354AZOM](/sequence-files/IGVFFI0354AZOM/), [IGVFFI5267KVMQ](/sequence-files/IGVFFI5267KVMQ/), [IGVFFI2727WQVS](/sequence-files/IGVFFI2727WQVS/), [IGVFFI6306UCPY](/sequence-files/IGVFFI6306UCPY/), [IGVFFI8883LRBT](/sequence-files/IGVFFI8883LRBT/), [IGVFFI2554OOEP](/sequence-files/IGVFFI2554OOEP/), [IGVFFI6079ATVH](/sequence-files/IGVFFI6079ATVH/), [IGVFFI4785RSVU](/sequence-files/IGVFFI4785RSVU/), [IGVFFI1656CXSA](/sequence-files/IGVFFI1656CXSA/), [IGVFFI5534AWYJ](/sequence-files/IGVFFI5534AWYJ/), [IGVFFI3329KNCB](/sequence-files/IGVFFI3329KNCB/), [IGVFFI3101HSEU](/sequence-files/IGVFFI3101HSEU/), [IGVFFI6312OYBZ](/sequence-files/IGVFFI6312OYBZ/), [IGVFFI8870KVMB](/sequence-files/IGVFFI8870KVMB/), [IGVFFI3793DPQT](/sequence-files/IGVFFI3793DPQT/), [IGVFFI9518UFDV](/sequence-files/IGVFFI9518UFDV/), [IGVFFI4924BALH](/sequence-files/IGVFFI4924BALH/), [IGVFFI3781UEFZ](/sequence-files/IGVFFI3781UEFZ/) 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/IGVFDS6359FZHI/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6359FZHI](/auxiliary-sets/IGVFDS6359FZHI/) has sequence file(s) [IGVFFI3043STQW](/sequence-files/IGVFFI3043STQW/), [IGVFFI6997XITK](/sequence-files/IGVFFI6997XITK/), [IGVFFI5278LQAY](/sequence-files/IGVFFI5278LQAY/), [IGVFFI5180CXKH](/sequence-files/IGVFFI5180CXKH/), [IGVFFI8745VLNT](/sequence-files/IGVFFI8745VLNT/), [IGVFFI3066LWHM](/sequence-files/IGVFFI3066LWHM/), [IGVFFI9429JMOJ](/sequence-files/IGVFFI9429JMOJ/), [IGVFFI5607TJVZ](/sequence-files/IGVFFI5607TJVZ/), [IGVFFI9742SYME](/sequence-files/IGVFFI9742SYME/), [IGVFFI7338DWWK](/sequence-files/IGVFFI7338DWWK/), [IGVFFI6399PGJQ](/sequence-files/IGVFFI6399PGJQ/), [IGVFFI6401MICT](/sequence-files/IGVFFI6401MICT/), [IGVFFI4807AAZI](/sequence-files/IGVFFI4807AAZI/), [IGVFFI7350UQLW](/sequence-files/IGVFFI7350UQLW/), [IGVFFI6213BYUY](/sequence-files/IGVFFI6213BYUY/), [IGVFFI9207IDMM](/sequence-files/IGVFFI9207IDMM/), [IGVFFI7121SZJD](/sequence-files/IGVFFI7121SZJD/), [IGVFFI7747ROLT](/sequence-files/IGVFFI7747ROLT/), [IGVFFI3609QXCK](/sequence-files/IGVFFI3609QXCK/), [IGVFFI0938WPJU](/sequence-files/IGVFFI0938WPJU/), [IGVFFI5747LSNL](/sequence-files/IGVFFI5747LSNL/), [IGVFFI0018FVXE](/sequence-files/IGVFFI0018FVXE/), [IGVFFI6612TAEI](/sequence-files/IGVFFI6612TAEI/), [IGVFFI0174HPHA](/sequence-files/IGVFFI0174HPHA/), [IGVFFI5168KASR](/sequence-files/IGVFFI5168KASR/), [IGVFFI0555LQIR](/sequence-files/IGVFFI0555LQIR/), [IGVFFI1078IQWD](/sequence-files/IGVFFI1078IQWD/), [IGVFFI2217TFSA](/sequence-files/IGVFFI2217TFSA/), [IGVFFI0071ZIGG](/sequence-files/IGVFFI0071ZIGG/), [IGVFFI2303HBSE](/sequence-files/IGVFFI2303HBSE/), [IGVFFI0354AZOM](/sequence-files/IGVFFI0354AZOM/), [IGVFFI5267KVMQ](/sequence-files/IGVFFI5267KVMQ/), [IGVFFI2727WQVS](/sequence-files/IGVFFI2727WQVS/), [IGVFFI6306UCPY](/sequence-files/IGVFFI6306UCPY/), [IGVFFI8883LRBT](/sequence-files/IGVFFI8883LRBT/), [IGVFFI2554OOEP](/sequence-files/IGVFFI2554OOEP/), [IGVFFI6079ATVH](/sequence-files/IGVFFI6079ATVH/), [IGVFFI4785RSVU](/sequence-files/IGVFFI4785RSVU/), [IGVFFI1656CXSA](/sequence-files/IGVFFI1656CXSA/), [IGVFFI5534AWYJ](/sequence-files/IGVFFI5534AWYJ/), [IGVFFI3329KNCB](/sequence-files/IGVFFI3329KNCB/), [IGVFFI3101HSEU](/sequence-files/IGVFFI3101HSEU/), [IGVFFI6312OYBZ](/sequence-files/IGVFFI6312OYBZ/), [IGVFFI8870KVMB](/sequence-files/IGVFFI8870KVMB/), [IGVFFI3793DPQT](/sequence-files/IGVFFI3793DPQT/), [IGVFFI9518UFDV](/sequence-files/IGVFFI9518UFDV/), [IGVFFI4924BALH](/sequence-files/IGVFFI4924BALH/), [IGVFFI3781UEFZ](/sequence-files/IGVFFI3781UEFZ/) 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/IGVFDS6359FZHI/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6359FZHI](/auxiliary-sets/IGVFDS6359FZHI/) 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/IGVFDS6359FZHI/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6359FZHI/",
"accession": "IGVFDS6359FZHI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:02.992206+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": "2023-12-20T23:06:51.648464+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5844KEUJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5844KEUJ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinA"
],
"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 0-25% 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": "2023-12-05T22:29:50.050244+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": "e9fc1daf-59f0-47b4-bf37-4cb520190d19"
}