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IGVFFI4854DWEG

preview
validated
This object is in preview status. Metadata is subject to change until this object is released.
File Set
IGVFDS1824XDMU(CRISPR prime editing Variant-EFFECTS targeting IL2RA 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:IL2RA_promoter_tiling_Jurkat-Stimulation_Variant-EFFECTS_File_Standardized
md5sum
b765337b37be90768d15a783f67453fb
Content MD5sum
529a6f2e2ada8fff63fe8cb468045df1
File Size
5.8 KB
Submitted File Name
IL2RA_promoter_tiling_Jurkat-Stimulation_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

25 items
Sample Terms
Summary
InVitroSystem
Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 51-75% expression of IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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 IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, 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
5.9 KB
validated