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IGVFFI4057VSBO

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validated
This object is in preview status. Metadata is subject to change until this object is released.
File Set
IGVFDS5056OAGR(CRISPR prime editing Variant-EFFECTS targeting PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus with unsorted FACS input, untransfected controls)
Summary
GRCh38 variant effects
File Format
tsv
Content Type
variant effects
Aliases
jesse-engreitz:PPIF_promoter_8mer_insertion_THP1_Variant-EFFECTS_File_Standardized
md5sum
222e73a89c818aa9888bb3c004857bdb
Content MD5sum
359e698f629cac4960305aa99749c63f
File Size
2.8 KB
Submitted File Name
PPIF_promoter_8mer_insertion_THP1_VariantEffectsFile.tsv.gz
Checkfiles Version
v20
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).
Attribution
Jesse Engreitz, Stanford

Reference Source Details

Genome Assembly
GRCh38

File Format Specifications

1 item
Page
Description
Type
Download
Standardized File Format
Preview
This file type describes results from genome editing experiments that measure the effect of a variant on an endogenous gene in the genome.
file format specification

Samples

78 items
Sample Terms
Summary
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 55-65% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 35-45% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 55-65% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 35-45% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 55-65% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 35-45% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 55-65% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 35-45% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 80-90% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library

Files This File Derives From

1 item
Accession
File Set
File Format
Content Type
Lab
File Size
Upload Status
tsv
variant effects
Jesse Engreitz, Stanford
2.4 KB
validated