{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI1254NFRS/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI1254NFRS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1_Variant-EFFECTS_File_Standardized"
],
"assay_titles": [
"Variant-EFFECTS"
],
"assembly": "GRCh38",
"audit": {},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"barcode_map_for": [],
"checkfiles_version": "v20",
"content_md5sum": "4df148410ef58cdd16e151738fa26b3b",
"content_type": "variant effects",
"controlled_access": false,
"creation_timestamp": "2025-03-29T00:13:26.294539+00:00",
"derived_from": [
"/tabular-files/IGVFFI4434LXUU/"
],
"derived_manually": true,
"description": "Manually standardized output of Variant-EFFECTS pipeline, formatted for GRCh38 with SPDI variant IDs",
"file_format": "tsv",
"file_format_specifications": [
{
"@id": "/documents/9d0ad6fb-777c-4cb6-a1c4-8ff7a41b17a1/",
"description": "This file type describes results from genome editing experiments that measure the effect of a variant on an endogenous gene in the genome."
}
],
"file_set": {
"@id": "/analysis-sets/IGVFDS1132MKHT/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1132MKHT",
"data_use_limitation_summaries": [
"no certificate"
],
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8685IQCU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8685IQCU",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8935ZBHB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8935ZBHB",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM4813DYRJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4813DYRJ",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM4927UHAC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4927UHAC",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"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"
},
{
"@id": "/in-vitro-systems/IGVFSM3944GUBH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3944GUBH",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM5477MOJC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5477MOJC",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"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"
},
{
"@id": "/in-vitro-systems/IGVFSM7132GAPK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7132GAPK",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 76-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM7733IXMO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7733IXMO",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2289HGEI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2289HGEI",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM0397MOBU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0397MOBU",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8787PPBP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8787PPBP",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8432ARFA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8432ARFA",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"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"
},
{
"@id": "/in-vitro-systems/IGVFSM3742TXQB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3742TXQB",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM7281WHSE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7281WHSE",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"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"
},
{
"@id": "/in-vitro-systems/IGVFSM9443MCAM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9443MCAM",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 76-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9514CCZH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9514CCZH",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 76-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM1066TJDA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1066TJDA",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2543EYOC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2543EYOC",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 76-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM7040CAHB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7040CAHB",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM5494BFWK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5494BFWK",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2125QBFY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2125QBFY",
"classifications": [
"cell line"
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"status": "preview",
"summary": "CRISPR prime editing Variant-EFFECTS targeting PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
},
"file_size": 328,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI1254NFRS/@@download/IGVFFI1254NFRS.tsv.gz",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"loci_list_for": [],
"md5sum": "2541ad86a7350ad21f4fd796276086f3",
"primer_design_for": [],
"quality_metrics": [],
"s3_uri": "s3://igvf-files/2025/03/29/bca12f48-a873-4a05-adab-3dddf856035e/IGVFFI1254NFRS.tsv.gz",
"schema_version": "15",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_file_name": "PPIF_5PrimeSpliceIndividual_AGGT_CAAC_VariantEffectsFile.tsv.gz",
"submitter_comment": "The original outputs from the Variant-EFFECTS pipeline report VariantIDs in the hg19 format. To obtain the standardized variant information provided in this file, hg19 coordinates were lifted to hg38 using the UCSC LiftOver tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver). Then, canonical, validated SPDIs were generated and validated using the igvf_spdi_demo tool (https://github.com/mikelove/igvf_spdi_demo).",
"summary": "GRCh38 variant effects",
"upload_status": "validated",
"uuid": "bca12f48-a873-4a05-adab-3dddf856035e"
}