{
"@context": "/terms/",
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"FileSet",
"Item"
],
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"aliases": [
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],
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"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
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"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5532ZGWU](/measurement-sets/IGVFDS5532ZGWU/) has sequence file(s) [IGVFFI8210XXJZ](/sequence-files/IGVFFI8210XXJZ/), [IGVFFI9958CGQM](/sequence-files/IGVFFI9958CGQM/), [IGVFFI8975UTAA](/sequence-files/IGVFFI8975UTAA/), [IGVFFI2056UEWK](/sequence-files/IGVFFI2056UEWK/), [IGVFFI5224BGBK](/sequence-files/IGVFFI5224BGBK/), [IGVFFI8661NHMC](/sequence-files/IGVFFI8661NHMC/), [IGVFFI2146ORDS](/sequence-files/IGVFFI2146ORDS/), [IGVFFI8754RXNF](/sequence-files/IGVFFI8754RXNF/), [IGVFFI5903APJV](/sequence-files/IGVFFI5903APJV/), [IGVFFI8768VZWA](/sequence-files/IGVFFI8768VZWA/), [IGVFFI7922ENJU](/sequence-files/IGVFFI7922ENJU/), [IGVFFI2172IKHA](/sequence-files/IGVFFI2172IKHA/), [IGVFFI5884JDLP](/sequence-files/IGVFFI5884JDLP/), [IGVFFI8556PLFS](/sequence-files/IGVFFI8556PLFS/), [IGVFFI2695TRGA](/sequence-files/IGVFFI2695TRGA/), [IGVFFI2649MNMI](/sequence-files/IGVFFI2649MNMI/) 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/IGVFDS5532ZGWU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5532ZGWU](/measurement-sets/IGVFDS5532ZGWU/) has sequence file(s): [IGVFFI8210XXJZ](/sequence-files/IGVFFI8210XXJZ/), [IGVFFI9958CGQM](/sequence-files/IGVFFI9958CGQM/), [IGVFFI8975UTAA](/sequence-files/IGVFFI8975UTAA/), [IGVFFI2056UEWK](/sequence-files/IGVFFI2056UEWK/), [IGVFFI5224BGBK](/sequence-files/IGVFFI5224BGBK/), [IGVFFI8661NHMC](/sequence-files/IGVFFI8661NHMC/), [IGVFFI2146ORDS](/sequence-files/IGVFFI2146ORDS/), [IGVFFI8754RXNF](/sequence-files/IGVFFI8754RXNF/), [IGVFFI5903APJV](/sequence-files/IGVFFI5903APJV/), [IGVFFI8768VZWA](/sequence-files/IGVFFI8768VZWA/), [IGVFFI7922ENJU](/sequence-files/IGVFFI7922ENJU/), [IGVFFI2172IKHA](/sequence-files/IGVFFI2172IKHA/), [IGVFFI5884JDLP](/sequence-files/IGVFFI5884JDLP/), [IGVFFI8556PLFS](/sequence-files/IGVFFI8556PLFS/), [IGVFFI2695TRGA](/sequence-files/IGVFFI2695TRGA/), [IGVFFI2649MNMI](/sequence-files/IGVFFI2649MNMI/) 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/IGVFDS5532ZGWU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5532ZGWU](/measurement-sets/IGVFDS5532ZGWU/) 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/IGVFDS5532ZGWU/"
}
]
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"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:26:02.146234+00:00",
"file_format": "fastq",
"file_size": 7439095,
"href": "/sequence-files/IGVFFI2649MNMI/@@download/IGVFFI2649MNMI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/0f2a0592-ca07-4627-bb2e-6b1559ff5c42/IGVFFI2649MNMI.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_pool-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinD-PCRrep2_S730_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7090INDM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6968KDVD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6968KDVD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep1-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5639ITBS/",
"accession": "IGVFDS5639ITBS",
"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 76-100% 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": "2024-12-01T20:58:54.101251+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": "871e0962-566f-49e4-9a05-13e038d7fe84"
}