{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9381QGYL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9381QGYL",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFSM2175KOEY](/in-vitro-systems/IGVFSM2175KOEY/) 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/IGVFSM2175KOEY/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9381QGYL](/measurement-sets/IGVFDS9381QGYL/) has in progress subobject auxiliary set [IGVFDS6553GFZB](/auxiliary-sets/IGVFDS6553GFZB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9381QGYL/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6553GFZB](/auxiliary-sets/IGVFDS6553GFZB/) has sequence file(s): [IGVFFI2924HYNO](/sequence-files/IGVFFI2924HYNO/), [IGVFFI1687AQIM](/sequence-files/IGVFFI1687AQIM/), [IGVFFI9808OVLJ](/sequence-files/IGVFFI9808OVLJ/), [IGVFFI4852GHJP](/sequence-files/IGVFFI4852GHJP/), [IGVFFI9524QHTO](/sequence-files/IGVFFI9524QHTO/), [IGVFFI9725WUTH](/sequence-files/IGVFFI9725WUTH/), [IGVFFI0634IPML](/sequence-files/IGVFFI0634IPML/), [IGVFFI6047UCAM](/sequence-files/IGVFFI6047UCAM/), [IGVFFI0346PFTX](/sequence-files/IGVFFI0346PFTX/), [IGVFFI7110RRRE](/sequence-files/IGVFFI7110RRRE/), [IGVFFI9402KQMY](/sequence-files/IGVFFI9402KQMY/), [IGVFFI6983PXUZ](/sequence-files/IGVFFI6983PXUZ/), [IGVFFI1966ORWS](/sequence-files/IGVFFI1966ORWS/), [IGVFFI3640WYRU](/sequence-files/IGVFFI3640WYRU/), [IGVFFI3879ALXZ](/sequence-files/IGVFFI3879ALXZ/), [IGVFFI5356GWER](/sequence-files/IGVFFI5356GWER/), [IGVFFI2781TBIG](/sequence-files/IGVFFI2781TBIG/), [IGVFFI5167VAFJ](/sequence-files/IGVFFI5167VAFJ/), [IGVFFI5478QGDN](/sequence-files/IGVFFI5478QGDN/), [IGVFFI1585QWET](/sequence-files/IGVFFI1585QWET/), [IGVFFI4270YUDC](/sequence-files/IGVFFI4270YUDC/), [IGVFFI4287YWHI](/sequence-files/IGVFFI4287YWHI/), [IGVFFI9497BBLJ](/sequence-files/IGVFFI9497BBLJ/), [IGVFFI1960ESWO](/sequence-files/IGVFFI1960ESWO/), [IGVFFI7577TTSA](/sequence-files/IGVFFI7577TTSA/), [IGVFFI4608HSLS](/sequence-files/IGVFFI4608HSLS/), [IGVFFI8714LANI](/sequence-files/IGVFFI8714LANI/), [IGVFFI8012RSML](/sequence-files/IGVFFI8012RSML/), [IGVFFI6632MKGP](/sequence-files/IGVFFI6632MKGP/), [IGVFFI1366FCMB](/sequence-files/IGVFFI1366FCMB/), [IGVFFI8260HFWJ](/sequence-files/IGVFFI8260HFWJ/), [IGVFFI3338KEAW](/sequence-files/IGVFFI3338KEAW/), [IGVFFI6966HDZC](/sequence-files/IGVFFI6966HDZC/), [IGVFFI5420TYCM](/sequence-files/IGVFFI5420TYCM/), [IGVFFI9484UUOC](/sequence-files/IGVFFI9484UUOC/), [IGVFFI0206BXVL](/sequence-files/IGVFFI0206BXVL/), [IGVFFI8386TEDH](/sequence-files/IGVFFI8386TEDH/), [IGVFFI4969BYGH](/sequence-files/IGVFFI4969BYGH/), [IGVFFI6494YIJY](/sequence-files/IGVFFI6494YIJY/), [IGVFFI7389SJVG](/sequence-files/IGVFFI7389SJVG/), [IGVFFI3535BCRZ](/sequence-files/IGVFFI3535BCRZ/), [IGVFFI4699UFBK](/sequence-files/IGVFFI4699UFBK/), [IGVFFI6748CQCZ](/sequence-files/IGVFFI6748CQCZ/), [IGVFFI4528QCPU](/sequence-files/IGVFFI4528QCPU/), [IGVFFI0614TWOQ](/sequence-files/IGVFFI0614TWOQ/), [IGVFFI3620RRIV](/sequence-files/IGVFFI3620RRIV/), [IGVFFI8362EEHI](/sequence-files/IGVFFI8362EEHI/), [IGVFFI8624OQLF](/sequence-files/IGVFFI8624OQLF/) 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/IGVFDS6553GFZB/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9381QGYL](/measurement-sets/IGVFDS9381QGYL/) 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/IGVFDS9381QGYL/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6553GFZB](/auxiliary-sets/IGVFDS6553GFZB/) has sequence file(s) [IGVFFI2924HYNO](/sequence-files/IGVFFI2924HYNO/), [IGVFFI1687AQIM](/sequence-files/IGVFFI1687AQIM/), [IGVFFI9808OVLJ](/sequence-files/IGVFFI9808OVLJ/), [IGVFFI4852GHJP](/sequence-files/IGVFFI4852GHJP/), [IGVFFI9524QHTO](/sequence-files/IGVFFI9524QHTO/), [IGVFFI9725WUTH](/sequence-files/IGVFFI9725WUTH/), [IGVFFI0634IPML](/sequence-files/IGVFFI0634IPML/), [IGVFFI6047UCAM](/sequence-files/IGVFFI6047UCAM/), [IGVFFI0346PFTX](/sequence-files/IGVFFI0346PFTX/), [IGVFFI7110RRRE](/sequence-files/IGVFFI7110RRRE/), [IGVFFI9402KQMY](/sequence-files/IGVFFI9402KQMY/), [IGVFFI6983PXUZ](/sequence-files/IGVFFI6983PXUZ/), [IGVFFI1966ORWS](/sequence-files/IGVFFI1966ORWS/), [IGVFFI3640WYRU](/sequence-files/IGVFFI3640WYRU/), [IGVFFI3879ALXZ](/sequence-files/IGVFFI3879ALXZ/), [IGVFFI5356GWER](/sequence-files/IGVFFI5356GWER/), [IGVFFI2781TBIG](/sequence-files/IGVFFI2781TBIG/), [IGVFFI5167VAFJ](/sequence-files/IGVFFI5167VAFJ/), [IGVFFI5478QGDN](/sequence-files/IGVFFI5478QGDN/), [IGVFFI1585QWET](/sequence-files/IGVFFI1585QWET/), [IGVFFI4270YUDC](/sequence-files/IGVFFI4270YUDC/), [IGVFFI4287YWHI](/sequence-files/IGVFFI4287YWHI/), [IGVFFI9497BBLJ](/sequence-files/IGVFFI9497BBLJ/), [IGVFFI1960ESWO](/sequence-files/IGVFFI1960ESWO/), [IGVFFI7577TTSA](/sequence-files/IGVFFI7577TTSA/), [IGVFFI4608HSLS](/sequence-files/IGVFFI4608HSLS/), [IGVFFI8714LANI](/sequence-files/IGVFFI8714LANI/), [IGVFFI8012RSML](/sequence-files/IGVFFI8012RSML/), [IGVFFI6632MKGP](/sequence-files/IGVFFI6632MKGP/), [IGVFFI1366FCMB](/sequence-files/IGVFFI1366FCMB/), [IGVFFI8260HFWJ](/sequence-files/IGVFFI8260HFWJ/), [IGVFFI3338KEAW](/sequence-files/IGVFFI3338KEAW/), [IGVFFI6966HDZC](/sequence-files/IGVFFI6966HDZC/), [IGVFFI5420TYCM](/sequence-files/IGVFFI5420TYCM/), [IGVFFI9484UUOC](/sequence-files/IGVFFI9484UUOC/), [IGVFFI0206BXVL](/sequence-files/IGVFFI0206BXVL/), [IGVFFI8386TEDH](/sequence-files/IGVFFI8386TEDH/), [IGVFFI4969BYGH](/sequence-files/IGVFFI4969BYGH/), [IGVFFI6494YIJY](/sequence-files/IGVFFI6494YIJY/), [IGVFFI7389SJVG](/sequence-files/IGVFFI7389SJVG/), [IGVFFI3535BCRZ](/sequence-files/IGVFFI3535BCRZ/), [IGVFFI4699UFBK](/sequence-files/IGVFFI4699UFBK/), [IGVFFI6748CQCZ](/sequence-files/IGVFFI6748CQCZ/), [IGVFFI4528QCPU](/sequence-files/IGVFFI4528QCPU/), [IGVFFI0614TWOQ](/sequence-files/IGVFFI0614TWOQ/), [IGVFFI3620RRIV](/sequence-files/IGVFFI3620RRIV/), [IGVFFI8362EEHI](/sequence-files/IGVFFI8362EEHI/), [IGVFFI8624OQLF](/sequence-files/IGVFFI8624OQLF/) 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/IGVFDS6553GFZB/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6553GFZB](/auxiliary-sets/IGVFDS6553GFZB/) 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/IGVFDS6553GFZB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6553GFZB/",
"accession": "IGVFDS6553GFZB",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:36.894323+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": "2023-12-20T23:07:31.364076+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2175KOEY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2175KOEY",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinC"
],
"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 51-75% 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": "2023-12-13T08:16:46.764673+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": "477191d3-b8df-4695-86e6-3899aa507cb0"
}