{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0561TMHL/",
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"MeasurementSet",
"FileSet",
"Item"
],
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"aliases": [
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],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
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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 [IGVFDS0561TMHL](/measurement-sets/IGVFDS0561TMHL/) has sequence file(s) [IGVFFI3250DRHR](/sequence-files/IGVFFI3250DRHR/), [IGVFFI0965TDOY](/sequence-files/IGVFFI0965TDOY/), [IGVFFI2890GIYA](/sequence-files/IGVFFI2890GIYA/), [IGVFFI2867MZFH](/sequence-files/IGVFFI2867MZFH/), [IGVFFI1584JSLG](/sequence-files/IGVFFI1584JSLG/), [IGVFFI0705VMDB](/sequence-files/IGVFFI0705VMDB/), [IGVFFI6873VMVY](/sequence-files/IGVFFI6873VMVY/), [IGVFFI3996DDJK](/sequence-files/IGVFFI3996DDJK/), [IGVFFI0177IBFC](/sequence-files/IGVFFI0177IBFC/), [IGVFFI9025DKAN](/sequence-files/IGVFFI9025DKAN/), [IGVFFI6565NPOG](/sequence-files/IGVFFI6565NPOG/), [IGVFFI1458GIKC](/sequence-files/IGVFFI1458GIKC/), [IGVFFI7417ZHAA](/sequence-files/IGVFFI7417ZHAA/), [IGVFFI7449HGLT](/sequence-files/IGVFFI7449HGLT/), [IGVFFI7772PQMF](/sequence-files/IGVFFI7772PQMF/), [IGVFFI8170ZADS](/sequence-files/IGVFFI8170ZADS/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS0561TMHL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0561TMHL](/measurement-sets/IGVFDS0561TMHL/) has sequence file(s): [IGVFFI3250DRHR](/sequence-files/IGVFFI3250DRHR/), [IGVFFI0965TDOY](/sequence-files/IGVFFI0965TDOY/), [IGVFFI2890GIYA](/sequence-files/IGVFFI2890GIYA/), [IGVFFI2867MZFH](/sequence-files/IGVFFI2867MZFH/), [IGVFFI1584JSLG](/sequence-files/IGVFFI1584JSLG/), [IGVFFI0705VMDB](/sequence-files/IGVFFI0705VMDB/), [IGVFFI6873VMVY](/sequence-files/IGVFFI6873VMVY/), [IGVFFI3996DDJK](/sequence-files/IGVFFI3996DDJK/), [IGVFFI0177IBFC](/sequence-files/IGVFFI0177IBFC/), [IGVFFI9025DKAN](/sequence-files/IGVFFI9025DKAN/), [IGVFFI6565NPOG](/sequence-files/IGVFFI6565NPOG/), [IGVFFI1458GIKC](/sequence-files/IGVFFI1458GIKC/), [IGVFFI7417ZHAA](/sequence-files/IGVFFI7417ZHAA/), [IGVFFI7449HGLT](/sequence-files/IGVFFI7449HGLT/), [IGVFFI7772PQMF](/sequence-files/IGVFFI7772PQMF/), [IGVFFI8170ZADS](/sequence-files/IGVFFI8170ZADS/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS0561TMHL/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0561TMHL](/measurement-sets/IGVFDS0561TMHL/) 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/IGVFDS0561TMHL/"
}
]
},
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"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
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}
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{
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}
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}
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"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinC-PCRrep1_S781_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7772PQMF/",
"accession": "IGVFFI7772PQMF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-BinC-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:10:25.731138+00:00",
"file_format": "fastq",
"file_size": 2705085,
"href": "/sequence-files/IGVFFI7772PQMF/@@download/IGVFFI7772PQMF.fastq.gz",
"md5sum": "a6d74150f0e337ffb7848918358a3cda",
"s3_uri": "s3://igvf-files/2024/12/11/1c783d66-d122-4ebe-b9d1-9e9db0a783ef/IGVFFI7772PQMF.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinC-PCRrep3_S805_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8170ZADS/",
"accession": "IGVFFI8170ZADS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-BinC-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:12:48.053830+00:00",
"file_format": "fastq",
"file_size": 3317577,
"href": "/sequence-files/IGVFFI8170ZADS/@@download/IGVFFI8170ZADS.fastq.gz",
"md5sum": "1dc52f8e226164a9a39ae045b5cb8681",
"s3_uri": "s3://igvf-files/2024/12/11/f0e078e6-8e4b-4181-9f88-8556fa447d30/IGVFFI8170ZADS.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinC-PCRrep4_S817_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8267JJHO/"
],
"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/IGVFSM3818WNVA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3818WNVA",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-BinC"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
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"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-11T00:09:15.480143+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF 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": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "7ac0ea16-5ec4-4a7e-a1e6-4273424a11fb"
}