{
"@context": "/terms/",
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"FileSet",
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],
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"aliases": [
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],
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"status": "released",
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},
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"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2985LAQO](/measurement-sets/IGVFDS2985LAQO/) has sequence file(s) [IGVFFI1529LGLF](/sequence-files/IGVFFI1529LGLF/), [IGVFFI9637HYGJ](/sequence-files/IGVFFI9637HYGJ/), [IGVFFI9130QSIR](/sequence-files/IGVFFI9130QSIR/), [IGVFFI8756ZUJN](/sequence-files/IGVFFI8756ZUJN/), [IGVFFI8752YUNZ](/sequence-files/IGVFFI8752YUNZ/), [IGVFFI2987HALG](/sequence-files/IGVFFI2987HALG/), [IGVFFI2752WRGG](/sequence-files/IGVFFI2752WRGG/), [IGVFFI9969QFQC](/sequence-files/IGVFFI9969QFQC/), [IGVFFI7903DRAS](/sequence-files/IGVFFI7903DRAS/), [IGVFFI5755CQDK](/sequence-files/IGVFFI5755CQDK/), [IGVFFI7028YBEP](/sequence-files/IGVFFI7028YBEP/), [IGVFFI6919TWGJ](/sequence-files/IGVFFI6919TWGJ/), [IGVFFI3430DNPG](/sequence-files/IGVFFI3430DNPG/), [IGVFFI5591IKOK](/sequence-files/IGVFFI5591IKOK/), [IGVFFI7283VOQF](/sequence-files/IGVFFI7283VOQF/), [IGVFFI0062OYFH](/sequence-files/IGVFFI0062OYFH/) 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/IGVFDS2985LAQO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2985LAQO](/measurement-sets/IGVFDS2985LAQO/) has sequence file(s): [IGVFFI1529LGLF](/sequence-files/IGVFFI1529LGLF/), [IGVFFI9637HYGJ](/sequence-files/IGVFFI9637HYGJ/), [IGVFFI9130QSIR](/sequence-files/IGVFFI9130QSIR/), [IGVFFI8756ZUJN](/sequence-files/IGVFFI8756ZUJN/), [IGVFFI8752YUNZ](/sequence-files/IGVFFI8752YUNZ/), [IGVFFI2987HALG](/sequence-files/IGVFFI2987HALG/), [IGVFFI2752WRGG](/sequence-files/IGVFFI2752WRGG/), [IGVFFI9969QFQC](/sequence-files/IGVFFI9969QFQC/), [IGVFFI7903DRAS](/sequence-files/IGVFFI7903DRAS/), [IGVFFI5755CQDK](/sequence-files/IGVFFI5755CQDK/), [IGVFFI7028YBEP](/sequence-files/IGVFFI7028YBEP/), [IGVFFI6919TWGJ](/sequence-files/IGVFFI6919TWGJ/), [IGVFFI3430DNPG](/sequence-files/IGVFFI3430DNPG/), [IGVFFI5591IKOK](/sequence-files/IGVFFI5591IKOK/), [IGVFFI7283VOQF](/sequence-files/IGVFFI7283VOQF/), [IGVFFI0062OYFH](/sequence-files/IGVFFI0062OYFH/) 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/IGVFDS2985LAQO/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2985LAQO](/measurement-sets/IGVFDS2985LAQO/) 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/IGVFDS2985LAQO/"
}
]
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"accession": "IGVFFI0062OYFH",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-BinB-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:08:27.333467+00:00",
"file_format": "fastq",
"file_size": 4452584,
"href": "/sequence-files/IGVFFI0062OYFH/@@download/IGVFFI0062OYFH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/8b4d3306-965c-4f70-82c2-2479d358a93d/IGVFFI0062OYFH.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-BioRep1-FFrep1-BinB-PCRrep4_S744_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/IGVFSM5285FOQN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5285FOQN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-BinB"
],
"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 26-50% 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": "2024-12-01T20:34:37.439410+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": "7250f639-6584-4da3-97af-bb720251fade"
}