{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3465JQXG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3465JQXG",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3465JQXG](/measurement-sets/IGVFDS3465JQXG/) has sequence file(s) [IGVFFI7856CVGD](/sequence-files/IGVFFI7856CVGD/), [IGVFFI2364MYCD](/sequence-files/IGVFFI2364MYCD/), [IGVFFI1009QSPW](/sequence-files/IGVFFI1009QSPW/), [IGVFFI6125LNYA](/sequence-files/IGVFFI6125LNYA/), [IGVFFI1073ATRZ](/sequence-files/IGVFFI1073ATRZ/), [IGVFFI0219BOCG](/sequence-files/IGVFFI0219BOCG/), [IGVFFI0839MJWJ](/sequence-files/IGVFFI0839MJWJ/), [IGVFFI4770UACM](/sequence-files/IGVFFI4770UACM/) 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/IGVFDS3465JQXG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3465JQXG](/measurement-sets/IGVFDS3465JQXG/) has sequence file(s): [IGVFFI7856CVGD](/sequence-files/IGVFFI7856CVGD/), [IGVFFI2364MYCD](/sequence-files/IGVFFI2364MYCD/), [IGVFFI1009QSPW](/sequence-files/IGVFFI1009QSPW/), [IGVFFI6125LNYA](/sequence-files/IGVFFI6125LNYA/), [IGVFFI1073ATRZ](/sequence-files/IGVFFI1073ATRZ/), [IGVFFI0219BOCG](/sequence-files/IGVFFI0219BOCG/), [IGVFFI0839MJWJ](/sequence-files/IGVFFI0839MJWJ/), [IGVFFI4770UACM](/sequence-files/IGVFFI4770UACM/) 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/IGVFDS3465JQXG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3465JQXG](/measurement-sets/IGVFDS3465JQXG/) 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/IGVFDS3465JQXG/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
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{
"@id": "/measurement-sets/IGVFDS8210FQOO/",
"accession": "IGVFDS8210FQOO",
"aliases": [
"jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-10T22:33:19.749898+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI7856CVGD",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:54:37.059566+00:00",
"file_format": "fastq",
"file_size": 45290194,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI2364MYCD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
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"creation_timestamp": "2024-12-11T00:57:34.084628+00:00",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep2_S985_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1009QSPW/",
"accession": "IGVFFI1009QSPW",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T19:25:03.828575+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI1009QSPW/@@download/IGVFFI1009QSPW.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep1_S973_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6125LNYA/",
"accession": "IGVFFI6125LNYA",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T19:28:13.736253+00:00",
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"file_size": 40171750,
"href": "/sequence-files/IGVFFI6125LNYA/@@download/IGVFFI6125LNYA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/dd492f6f-564e-4006-aaad-c6f4cfbff121/IGVFFI6125LNYA.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_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep2_S985_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1073ATRZ/",
"accession": "IGVFFI1073ATRZ",
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"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
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"controlled_access": false,
"creation_timestamp": "2024-12-11T21:36:57.958225+00:00",
"file_format": "fastq",
"file_size": 16611081,
"href": "/sequence-files/IGVFFI1073ATRZ/@@download/IGVFFI1073ATRZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/99782083-d6b6-4b4b-9c54-e1e701014650/IGVFFI1073ATRZ.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_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep1_S973_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0219BOCG/",
"accession": "IGVFFI0219BOCG",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:53:05.733173+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI0219BOCG/@@download/IGVFFI0219BOCG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/2f6de745-5296-44fe-a35e-20f445f00e9a/IGVFFI0219BOCG.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0839MJWJ/",
"accession": "IGVFFI0839MJWJ",
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],
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"creation_timestamp": "2024-12-11T21:40:10.925610+00:00",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4770UACM/",
"accession": "IGVFFI4770UACM",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
],
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"creation_timestamp": "2024-12-11T23:49:57.931387+00:00",
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"term_name": "Illumina NovaSeq X"
},
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1132MKHT/"
],
"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/IGVFSM0397MOBU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0397MOBU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2432IDGC/",
"accession": "IGVFDS2432IDGC",
"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 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": "2024-12-11T00:54:37.059566+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": "65775dda-d8f8-4a29-8735-36e0f8fee470"
}