{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4141QOFR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4141QOFR",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-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 [IGVFDS4141QOFR](/measurement-sets/IGVFDS4141QOFR/) has in progress subobject auxiliary set [IGVFDS9897BTUJ](/auxiliary-sets/IGVFDS9897BTUJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4141QOFR/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0259SMPF](/in-vitro-systems/IGVFSM0259SMPF/) 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/IGVFSM0259SMPF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9897BTUJ](/auxiliary-sets/IGVFDS9897BTUJ/) has sequence file(s): [IGVFFI5398ROAM](/sequence-files/IGVFFI5398ROAM/), [IGVFFI4244WXGM](/sequence-files/IGVFFI4244WXGM/), [IGVFFI9778KPAU](/sequence-files/IGVFFI9778KPAU/), [IGVFFI2032BIJT](/sequence-files/IGVFFI2032BIJT/), [IGVFFI6001DMDJ](/sequence-files/IGVFFI6001DMDJ/), [IGVFFI3018SSEY](/sequence-files/IGVFFI3018SSEY/), [IGVFFI0220HAFC](/sequence-files/IGVFFI0220HAFC/), [IGVFFI7917KPBJ](/sequence-files/IGVFFI7917KPBJ/), [IGVFFI8185JOGB](/sequence-files/IGVFFI8185JOGB/), [IGVFFI1738HIPM](/sequence-files/IGVFFI1738HIPM/), [IGVFFI1588VVFK](/sequence-files/IGVFFI1588VVFK/), [IGVFFI3790CZIF](/sequence-files/IGVFFI3790CZIF/), [IGVFFI5887KXBV](/sequence-files/IGVFFI5887KXBV/), [IGVFFI2390PFXK](/sequence-files/IGVFFI2390PFXK/), [IGVFFI6716WRFX](/sequence-files/IGVFFI6716WRFX/), [IGVFFI6910SIEW](/sequence-files/IGVFFI6910SIEW/), [IGVFFI1295YHHN](/sequence-files/IGVFFI1295YHHN/), [IGVFFI5310QJQU](/sequence-files/IGVFFI5310QJQU/), [IGVFFI0789NOIT](/sequence-files/IGVFFI0789NOIT/), [IGVFFI8021ERKN](/sequence-files/IGVFFI8021ERKN/), [IGVFFI1252TTRQ](/sequence-files/IGVFFI1252TTRQ/), [IGVFFI2245ZYZS](/sequence-files/IGVFFI2245ZYZS/), [IGVFFI2777HKED](/sequence-files/IGVFFI2777HKED/), [IGVFFI2444LDZO](/sequence-files/IGVFFI2444LDZO/), [IGVFFI2015ODUP](/sequence-files/IGVFFI2015ODUP/), [IGVFFI0256WAGY](/sequence-files/IGVFFI0256WAGY/), [IGVFFI3271BSJD](/sequence-files/IGVFFI3271BSJD/), [IGVFFI2874QKKT](/sequence-files/IGVFFI2874QKKT/), [IGVFFI0557KAVN](/sequence-files/IGVFFI0557KAVN/), [IGVFFI4480KATX](/sequence-files/IGVFFI4480KATX/), [IGVFFI7244WSOU](/sequence-files/IGVFFI7244WSOU/), [IGVFFI3374SFEY](/sequence-files/IGVFFI3374SFEY/), [IGVFFI8471XDOD](/sequence-files/IGVFFI8471XDOD/), [IGVFFI4099OVNZ](/sequence-files/IGVFFI4099OVNZ/), [IGVFFI1047ZJWY](/sequence-files/IGVFFI1047ZJWY/), [IGVFFI6826TTLX](/sequence-files/IGVFFI6826TTLX/), [IGVFFI8798QLWP](/sequence-files/IGVFFI8798QLWP/), [IGVFFI3157QDGB](/sequence-files/IGVFFI3157QDGB/), [IGVFFI4965BEGQ](/sequence-files/IGVFFI4965BEGQ/), [IGVFFI4472MLSZ](/sequence-files/IGVFFI4472MLSZ/), [IGVFFI0906QXQF](/sequence-files/IGVFFI0906QXQF/), [IGVFFI1969NNZC](/sequence-files/IGVFFI1969NNZC/), [IGVFFI1429FYEG](/sequence-files/IGVFFI1429FYEG/), [IGVFFI4834ZJAB](/sequence-files/IGVFFI4834ZJAB/), [IGVFFI2586IXAF](/sequence-files/IGVFFI2586IXAF/), [IGVFFI3831ITLD](/sequence-files/IGVFFI3831ITLD/), [IGVFFI3799BWTY](/sequence-files/IGVFFI3799BWTY/), [IGVFFI2731JTVH](/sequence-files/IGVFFI2731JTVH/) 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/IGVFDS9897BTUJ/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4141QOFR](/measurement-sets/IGVFDS4141QOFR/) 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/IGVFDS4141QOFR/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9897BTUJ](/auxiliary-sets/IGVFDS9897BTUJ/) has sequence file(s) [IGVFFI5398ROAM](/sequence-files/IGVFFI5398ROAM/), [IGVFFI4244WXGM](/sequence-files/IGVFFI4244WXGM/), [IGVFFI9778KPAU](/sequence-files/IGVFFI9778KPAU/), [IGVFFI2032BIJT](/sequence-files/IGVFFI2032BIJT/), [IGVFFI6001DMDJ](/sequence-files/IGVFFI6001DMDJ/), [IGVFFI3018SSEY](/sequence-files/IGVFFI3018SSEY/), [IGVFFI0220HAFC](/sequence-files/IGVFFI0220HAFC/), [IGVFFI7917KPBJ](/sequence-files/IGVFFI7917KPBJ/), [IGVFFI8185JOGB](/sequence-files/IGVFFI8185JOGB/), [IGVFFI1738HIPM](/sequence-files/IGVFFI1738HIPM/), [IGVFFI1588VVFK](/sequence-files/IGVFFI1588VVFK/), [IGVFFI3790CZIF](/sequence-files/IGVFFI3790CZIF/), [IGVFFI5887KXBV](/sequence-files/IGVFFI5887KXBV/), [IGVFFI2390PFXK](/sequence-files/IGVFFI2390PFXK/), [IGVFFI6716WRFX](/sequence-files/IGVFFI6716WRFX/), [IGVFFI6910SIEW](/sequence-files/IGVFFI6910SIEW/), [IGVFFI1295YHHN](/sequence-files/IGVFFI1295YHHN/), [IGVFFI5310QJQU](/sequence-files/IGVFFI5310QJQU/), [IGVFFI0789NOIT](/sequence-files/IGVFFI0789NOIT/), [IGVFFI8021ERKN](/sequence-files/IGVFFI8021ERKN/), [IGVFFI1252TTRQ](/sequence-files/IGVFFI1252TTRQ/), [IGVFFI2245ZYZS](/sequence-files/IGVFFI2245ZYZS/), [IGVFFI2777HKED](/sequence-files/IGVFFI2777HKED/), [IGVFFI2444LDZO](/sequence-files/IGVFFI2444LDZO/), [IGVFFI2015ODUP](/sequence-files/IGVFFI2015ODUP/), [IGVFFI0256WAGY](/sequence-files/IGVFFI0256WAGY/), [IGVFFI3271BSJD](/sequence-files/IGVFFI3271BSJD/), [IGVFFI2874QKKT](/sequence-files/IGVFFI2874QKKT/), [IGVFFI0557KAVN](/sequence-files/IGVFFI0557KAVN/), [IGVFFI4480KATX](/sequence-files/IGVFFI4480KATX/), [IGVFFI7244WSOU](/sequence-files/IGVFFI7244WSOU/), [IGVFFI3374SFEY](/sequence-files/IGVFFI3374SFEY/), [IGVFFI8471XDOD](/sequence-files/IGVFFI8471XDOD/), [IGVFFI4099OVNZ](/sequence-files/IGVFFI4099OVNZ/), [IGVFFI1047ZJWY](/sequence-files/IGVFFI1047ZJWY/), [IGVFFI6826TTLX](/sequence-files/IGVFFI6826TTLX/), [IGVFFI8798QLWP](/sequence-files/IGVFFI8798QLWP/), [IGVFFI3157QDGB](/sequence-files/IGVFFI3157QDGB/), [IGVFFI4965BEGQ](/sequence-files/IGVFFI4965BEGQ/), [IGVFFI4472MLSZ](/sequence-files/IGVFFI4472MLSZ/), [IGVFFI0906QXQF](/sequence-files/IGVFFI0906QXQF/), [IGVFFI1969NNZC](/sequence-files/IGVFFI1969NNZC/), [IGVFFI1429FYEG](/sequence-files/IGVFFI1429FYEG/), [IGVFFI4834ZJAB](/sequence-files/IGVFFI4834ZJAB/), [IGVFFI2586IXAF](/sequence-files/IGVFFI2586IXAF/), [IGVFFI3831ITLD](/sequence-files/IGVFFI3831ITLD/), [IGVFFI3799BWTY](/sequence-files/IGVFFI3799BWTY/), [IGVFFI2731JTVH](/sequence-files/IGVFFI2731JTVH/) 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/IGVFDS9897BTUJ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9897BTUJ](/auxiliary-sets/IGVFDS9897BTUJ/) 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/IGVFDS9897BTUJ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9897BTUJ/",
"accession": "IGVFDS9897BTUJ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:46.366554+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": "2023-12-20T23:07:22.638357+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0259SMPF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0259SMPF",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinA"
],
"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 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": "2023-12-13T09:07:05.091798+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": "b19678ee-d555-4a83-a8fd-f45cc4ab7c16"
}