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IGVFFI3397AYBP

preview
validated
This object is in preview status. Metadata is subject to change until this object is released.
File Set
IGVFDS9162RHFP(CRISPR prime editing Variant-EFFECTS targeting PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus)
Summary
GRCh38 variant effects
File Format
tsv
Content Type
variant effects
Aliases
jesse-engreitz:PPIF_promoter_8mer_insertion_Jurkat-NoStimulation_Variant-EFFECTS_File_Standardized
md5sum
9ee5b73ba8f9da3067fe179ce9c0e1ab
Content MD5sum
7c17f5f572370a56fd8301e04f58cd95
File Size
2.7 KB
Submitted File Name
PPIF_promoter_8mer_insertion_Jurkat-NoStimulation_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

43 items
Sample Terms
Summary
InVitroSystem
Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 11-20% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) Jurkat 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
InVitroSystem
Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 0-10% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) Jurkat cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) Jurkat 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) Jurkat cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 90-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) Jurkat 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
InVitroSystem
Homo sapiens (male) Jurkat cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
InVitroSystem
Homo sapiens (male) Jurkat 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

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
2.8 KB
validated