{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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"aliases": [
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],
"assay_term": {
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"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6981TLKY](/measurement-sets/IGVFDS6981TLKY/) has sequence file(s) [IGVFFI6762MHSE](/sequence-files/IGVFFI6762MHSE/), [IGVFFI2155EKOT](/sequence-files/IGVFFI2155EKOT/), [IGVFFI4639YRRJ](/sequence-files/IGVFFI4639YRRJ/), [IGVFFI8501KWAS](/sequence-files/IGVFFI8501KWAS/), [IGVFFI8201QIKW](/sequence-files/IGVFFI8201QIKW/), [IGVFFI3351AUPZ](/sequence-files/IGVFFI3351AUPZ/), [IGVFFI3182TZLB](/sequence-files/IGVFFI3182TZLB/), [IGVFFI8244HASO](/sequence-files/IGVFFI8244HASO/), [IGVFFI1096QXXT](/sequence-files/IGVFFI1096QXXT/), [IGVFFI3303CSYQ](/sequence-files/IGVFFI3303CSYQ/), [IGVFFI7735OFJE](/sequence-files/IGVFFI7735OFJE/), [IGVFFI6457JUOJ](/sequence-files/IGVFFI6457JUOJ/), [IGVFFI5829CDBA](/sequence-files/IGVFFI5829CDBA/), [IGVFFI3455EDPF](/sequence-files/IGVFFI3455EDPF/), [IGVFFI7230SKVA](/sequence-files/IGVFFI7230SKVA/), [IGVFFI9595OSBQ](/sequence-files/IGVFFI9595OSBQ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS6981TLKY/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6981TLKY](/measurement-sets/IGVFDS6981TLKY/) has sequence file(s): [IGVFFI6762MHSE](/sequence-files/IGVFFI6762MHSE/), [IGVFFI2155EKOT](/sequence-files/IGVFFI2155EKOT/), [IGVFFI4639YRRJ](/sequence-files/IGVFFI4639YRRJ/), [IGVFFI8501KWAS](/sequence-files/IGVFFI8501KWAS/), [IGVFFI8201QIKW](/sequence-files/IGVFFI8201QIKW/), [IGVFFI3351AUPZ](/sequence-files/IGVFFI3351AUPZ/), [IGVFFI3182TZLB](/sequence-files/IGVFFI3182TZLB/), [IGVFFI8244HASO](/sequence-files/IGVFFI8244HASO/), [IGVFFI1096QXXT](/sequence-files/IGVFFI1096QXXT/), [IGVFFI3303CSYQ](/sequence-files/IGVFFI3303CSYQ/), [IGVFFI7735OFJE](/sequence-files/IGVFFI7735OFJE/), [IGVFFI6457JUOJ](/sequence-files/IGVFFI6457JUOJ/), [IGVFFI5829CDBA](/sequence-files/IGVFFI5829CDBA/), [IGVFFI3455EDPF](/sequence-files/IGVFFI3455EDPF/), [IGVFFI7230SKVA](/sequence-files/IGVFFI7230SKVA/), [IGVFFI9595OSBQ](/sequence-files/IGVFFI9595OSBQ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6981TLKY/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6981TLKY](/measurement-sets/IGVFDS6981TLKY/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS6981TLKY/"
}
]
},
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"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep3_S947_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9595OSBQ/",
"accession": "IGVFFI9595OSBQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:43:52.309965+00:00",
"file_format": "fastq",
"file_size": 1146846,
"href": "/sequence-files/IGVFFI9595OSBQ/@@download/IGVFFI9595OSBQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/12/c7014872-08fe-4c51-b0a1-5d2c56b240bb/IGVFFI9595OSBQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinA-PCRrep1_S923_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8174BPPS/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1138SBPT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1138SBPT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-BinA"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6555EOZU/",
"accession": "IGVFDS6555EOZU",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"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": "preview",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-11T16:49:21.838100+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"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": "9e116b2e-521c-4554-8b3c-1aff2b677cb6"
}