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IGVFFI5188DBPQ

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validated
This object is in preview status. Metadata is subject to change until this object is released.
File Set
IGVFDS6299IJHG(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_Enformer_edits_Jurkat_Variant-EFFECTS_File_Standardized
md5sum
0abdaa6581ad109dcc7298b64e1ce0a0
Content MD5sum
871c5115a1178c7751e6fd4e15832206
File Size
10 KB
Submitted File Name
PPIF_promoter_Enformer_edits_Jurkat_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

41 items
Sample Terms
Summary
InVitroSystem
Homo sapiens (male) Jurkat 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
InVitroSystem
Homo sapiens (male) Jurkat 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
InVitroSystem
Homo sapiens (male) Jurkat 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
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 76-100% 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 26-50% 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 51-75% 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 26-50% 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 26-50% 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
11 KB
validated