{
"@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 [IGVFDS7390OIZX](/measurement-sets/IGVFDS7390OIZX/) has sequence file(s) [IGVFFI1413MPDZ](/sequence-files/IGVFFI1413MPDZ/), [IGVFFI1649DKNW](/sequence-files/IGVFFI1649DKNW/), [IGVFFI2505DQMC](/sequence-files/IGVFFI2505DQMC/), [IGVFFI1600GYCA](/sequence-files/IGVFFI1600GYCA/), [IGVFFI5404APZM](/sequence-files/IGVFFI5404APZM/), [IGVFFI7015IOZQ](/sequence-files/IGVFFI7015IOZQ/), [IGVFFI7686HUFV](/sequence-files/IGVFFI7686HUFV/), [IGVFFI6379UYXS](/sequence-files/IGVFFI6379UYXS/), [IGVFFI1191PFDC](/sequence-files/IGVFFI1191PFDC/), [IGVFFI6490OAXO](/sequence-files/IGVFFI6490OAXO/), [IGVFFI0481KBQJ](/sequence-files/IGVFFI0481KBQJ/), [IGVFFI1874NAFS](/sequence-files/IGVFFI1874NAFS/), [IGVFFI4698ZIGI](/sequence-files/IGVFFI4698ZIGI/), [IGVFFI0226FDXW](/sequence-files/IGVFFI0226FDXW/), [IGVFFI5480EKDI](/sequence-files/IGVFFI5480EKDI/), [IGVFFI4005MVIO](/sequence-files/IGVFFI4005MVIO/) 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/IGVFDS7390OIZX/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7390OIZX](/measurement-sets/IGVFDS7390OIZX/) has sequence file(s): [IGVFFI1413MPDZ](/sequence-files/IGVFFI1413MPDZ/), [IGVFFI1649DKNW](/sequence-files/IGVFFI1649DKNW/), [IGVFFI2505DQMC](/sequence-files/IGVFFI2505DQMC/), [IGVFFI1600GYCA](/sequence-files/IGVFFI1600GYCA/), [IGVFFI5404APZM](/sequence-files/IGVFFI5404APZM/), [IGVFFI7015IOZQ](/sequence-files/IGVFFI7015IOZQ/), [IGVFFI7686HUFV](/sequence-files/IGVFFI7686HUFV/), [IGVFFI6379UYXS](/sequence-files/IGVFFI6379UYXS/), [IGVFFI1191PFDC](/sequence-files/IGVFFI1191PFDC/), [IGVFFI6490OAXO](/sequence-files/IGVFFI6490OAXO/), [IGVFFI0481KBQJ](/sequence-files/IGVFFI0481KBQJ/), [IGVFFI1874NAFS](/sequence-files/IGVFFI1874NAFS/), [IGVFFI4698ZIGI](/sequence-files/IGVFFI4698ZIGI/), [IGVFFI0226FDXW](/sequence-files/IGVFFI0226FDXW/), [IGVFFI5480EKDI](/sequence-files/IGVFFI5480EKDI/), [IGVFFI4005MVIO](/sequence-files/IGVFFI4005MVIO/) 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/IGVFDS7390OIZX/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7390OIZX](/measurement-sets/IGVFDS7390OIZX/) 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/IGVFDS7390OIZX/"
}
]
},
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},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
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"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinD-PCRrep3_S798_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4005MVIO/",
"accession": "IGVFFI4005MVIO",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:45:38.267035+00:00",
"file_format": "fastq",
"file_size": 2840783,
"href": "/sequence-files/IGVFFI4005MVIO/@@download/IGVFFI4005MVIO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/8e6afc32-3d6e-4cf0-8032-c9d72f3ead77/IGVFFI4005MVIO.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-BioRep1-FFrep1-BinD-PCRrep2_S786_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/IGVFSM8534GUZK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8534GUZK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9097TEUZ/",
"accession": "IGVFDS9097TEUZ",
"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": "2024-12-10T23:48:30.817201+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": "3d218af0-64f0-43d9-93fb-0d76259bc59f"
}