{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8099KDSE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8099KDSE",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_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 [IGVFDS8099KDSE](/measurement-sets/IGVFDS8099KDSE/) has in progress subobject auxiliary set [IGVFDS9966IXGW](/auxiliary-sets/IGVFDS9966IXGW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8099KDSE/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5640BXQI](/in-vitro-systems/IGVFSM5640BXQI/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5640BXQI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9966IXGW](/auxiliary-sets/IGVFDS9966IXGW/) has sequence file(s): [IGVFFI7333EFKT](/sequence-files/IGVFFI7333EFKT/), [IGVFFI2832YDAA](/sequence-files/IGVFFI2832YDAA/), [IGVFFI8740SNVN](/sequence-files/IGVFFI8740SNVN/), [IGVFFI8470OGTN](/sequence-files/IGVFFI8470OGTN/), [IGVFFI8501EIZU](/sequence-files/IGVFFI8501EIZU/), [IGVFFI3307SSNJ](/sequence-files/IGVFFI3307SSNJ/), [IGVFFI6833PBRT](/sequence-files/IGVFFI6833PBRT/), [IGVFFI7849NMYB](/sequence-files/IGVFFI7849NMYB/), [IGVFFI9242IGFF](/sequence-files/IGVFFI9242IGFF/), [IGVFFI9573XUTR](/sequence-files/IGVFFI9573XUTR/), [IGVFFI3892COUG](/sequence-files/IGVFFI3892COUG/), [IGVFFI8049JEBF](/sequence-files/IGVFFI8049JEBF/), [IGVFFI7224SQSW](/sequence-files/IGVFFI7224SQSW/), [IGVFFI2759SBEF](/sequence-files/IGVFFI2759SBEF/), [IGVFFI9511GFJI](/sequence-files/IGVFFI9511GFJI/), [IGVFFI6816LSQS](/sequence-files/IGVFFI6816LSQS/), [IGVFFI2585LKSN](/sequence-files/IGVFFI2585LKSN/), [IGVFFI5778YUEP](/sequence-files/IGVFFI5778YUEP/), [IGVFFI7656FUSL](/sequence-files/IGVFFI7656FUSL/), [IGVFFI5564UHRU](/sequence-files/IGVFFI5564UHRU/), [IGVFFI1101ZSHC](/sequence-files/IGVFFI1101ZSHC/), [IGVFFI5572OHAK](/sequence-files/IGVFFI5572OHAK/), [IGVFFI4567IFZE](/sequence-files/IGVFFI4567IFZE/), [IGVFFI9405TXNB](/sequence-files/IGVFFI9405TXNB/), [IGVFFI1769QRUG](/sequence-files/IGVFFI1769QRUG/), [IGVFFI1534ORTZ](/sequence-files/IGVFFI1534ORTZ/), [IGVFFI9040GPJJ](/sequence-files/IGVFFI9040GPJJ/), [IGVFFI3758UXBJ](/sequence-files/IGVFFI3758UXBJ/), [IGVFFI3260HHDS](/sequence-files/IGVFFI3260HHDS/), [IGVFFI6412EHVZ](/sequence-files/IGVFFI6412EHVZ/), [IGVFFI5003GOLI](/sequence-files/IGVFFI5003GOLI/), [IGVFFI3086OARI](/sequence-files/IGVFFI3086OARI/), [IGVFFI6476PSIF](/sequence-files/IGVFFI6476PSIF/), [IGVFFI5013GDPR](/sequence-files/IGVFFI5013GDPR/), [IGVFFI3406FCOT](/sequence-files/IGVFFI3406FCOT/), [IGVFFI5125BAJN](/sequence-files/IGVFFI5125BAJN/), [IGVFFI0549VBGU](/sequence-files/IGVFFI0549VBGU/), [IGVFFI5733WJWY](/sequence-files/IGVFFI5733WJWY/), [IGVFFI8687QXXN](/sequence-files/IGVFFI8687QXXN/), [IGVFFI8513HYAB](/sequence-files/IGVFFI8513HYAB/), [IGVFFI4080PVGA](/sequence-files/IGVFFI4080PVGA/), [IGVFFI2069FMAV](/sequence-files/IGVFFI2069FMAV/), [IGVFFI1502MCXO](/sequence-files/IGVFFI1502MCXO/), [IGVFFI7080VUZV](/sequence-files/IGVFFI7080VUZV/), [IGVFFI9945ZGUV](/sequence-files/IGVFFI9945ZGUV/), [IGVFFI7958QZDR](/sequence-files/IGVFFI7958QZDR/), [IGVFFI6249BZUU](/sequence-files/IGVFFI6249BZUU/), [IGVFFI5041JQIM](/sequence-files/IGVFFI5041JQIM/) 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/IGVFDS9966IXGW/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8099KDSE](/measurement-sets/IGVFDS8099KDSE/) 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/IGVFDS8099KDSE/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9966IXGW](/auxiliary-sets/IGVFDS9966IXGW/) has sequence file(s) [IGVFFI7333EFKT](/sequence-files/IGVFFI7333EFKT/), [IGVFFI2832YDAA](/sequence-files/IGVFFI2832YDAA/), [IGVFFI8740SNVN](/sequence-files/IGVFFI8740SNVN/), [IGVFFI8470OGTN](/sequence-files/IGVFFI8470OGTN/), [IGVFFI8501EIZU](/sequence-files/IGVFFI8501EIZU/), [IGVFFI3307SSNJ](/sequence-files/IGVFFI3307SSNJ/), [IGVFFI6833PBRT](/sequence-files/IGVFFI6833PBRT/), [IGVFFI7849NMYB](/sequence-files/IGVFFI7849NMYB/), [IGVFFI9242IGFF](/sequence-files/IGVFFI9242IGFF/), [IGVFFI9573XUTR](/sequence-files/IGVFFI9573XUTR/), [IGVFFI3892COUG](/sequence-files/IGVFFI3892COUG/), [IGVFFI8049JEBF](/sequence-files/IGVFFI8049JEBF/), [IGVFFI7224SQSW](/sequence-files/IGVFFI7224SQSW/), [IGVFFI2759SBEF](/sequence-files/IGVFFI2759SBEF/), [IGVFFI9511GFJI](/sequence-files/IGVFFI9511GFJI/), [IGVFFI6816LSQS](/sequence-files/IGVFFI6816LSQS/), [IGVFFI2585LKSN](/sequence-files/IGVFFI2585LKSN/), [IGVFFI5778YUEP](/sequence-files/IGVFFI5778YUEP/), [IGVFFI7656FUSL](/sequence-files/IGVFFI7656FUSL/), [IGVFFI5564UHRU](/sequence-files/IGVFFI5564UHRU/), [IGVFFI1101ZSHC](/sequence-files/IGVFFI1101ZSHC/), [IGVFFI5572OHAK](/sequence-files/IGVFFI5572OHAK/), [IGVFFI4567IFZE](/sequence-files/IGVFFI4567IFZE/), [IGVFFI9405TXNB](/sequence-files/IGVFFI9405TXNB/), [IGVFFI1769QRUG](/sequence-files/IGVFFI1769QRUG/), [IGVFFI1534ORTZ](/sequence-files/IGVFFI1534ORTZ/), [IGVFFI9040GPJJ](/sequence-files/IGVFFI9040GPJJ/), [IGVFFI3758UXBJ](/sequence-files/IGVFFI3758UXBJ/), [IGVFFI3260HHDS](/sequence-files/IGVFFI3260HHDS/), [IGVFFI6412EHVZ](/sequence-files/IGVFFI6412EHVZ/), [IGVFFI5003GOLI](/sequence-files/IGVFFI5003GOLI/), [IGVFFI3086OARI](/sequence-files/IGVFFI3086OARI/), [IGVFFI6476PSIF](/sequence-files/IGVFFI6476PSIF/), [IGVFFI5013GDPR](/sequence-files/IGVFFI5013GDPR/), [IGVFFI3406FCOT](/sequence-files/IGVFFI3406FCOT/), [IGVFFI5125BAJN](/sequence-files/IGVFFI5125BAJN/), [IGVFFI0549VBGU](/sequence-files/IGVFFI0549VBGU/), [IGVFFI5733WJWY](/sequence-files/IGVFFI5733WJWY/), [IGVFFI8687QXXN](/sequence-files/IGVFFI8687QXXN/), [IGVFFI8513HYAB](/sequence-files/IGVFFI8513HYAB/), [IGVFFI4080PVGA](/sequence-files/IGVFFI4080PVGA/), [IGVFFI2069FMAV](/sequence-files/IGVFFI2069FMAV/), [IGVFFI1502MCXO](/sequence-files/IGVFFI1502MCXO/), [IGVFFI7080VUZV](/sequence-files/IGVFFI7080VUZV/), [IGVFFI9945ZGUV](/sequence-files/IGVFFI9945ZGUV/), [IGVFFI7958QZDR](/sequence-files/IGVFFI7958QZDR/), [IGVFFI6249BZUU](/sequence-files/IGVFFI6249BZUU/), [IGVFFI5041JQIM](/sequence-files/IGVFFI5041JQIM/) 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/IGVFDS9966IXGW/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9966IXGW](/auxiliary-sets/IGVFDS9966IXGW/) 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/IGVFDS9966IXGW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9966IXGW/",
"accession": "IGVFDS9966IXGW",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:44.166757+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/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:35.402772+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5640BXQI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5640BXQI",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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 76-100% 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": "2023-12-13T08:50:49.511166+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": "07d32d12-bb5a-4640-b3e2-a3fe12510949"
}