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Series GSE212345 Query DataSets for GSE212345
Status Public on Sep 07, 2022
Title RNA-seq and methyl-seq of A20 mouse cells using a novel TETact activation of CD4
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Stably silenced genes that display a high level of CpG dinucleotide methylation are refractory to the current generation of CRISPR dCas9-based activation systems. To counter this, we created an improved activation system by coupling the catalytic domain of DNA demethylating enzyme TET1 with transcriptional activators (TETact). To evaluate the specificity of our TETact system, we conducted RNA-seq on A20 cells containing the TETact-v3 system targeting the CD4 promoter, along with non-targeting control TETact-v3 cells as well as wildtype A20. A20 is a BALB/C B cell lymphoma cell line that does not normally express CD4. Non-transduced A20 showed a very similar gene expression profile with the control TETact-v3 cells. Importantly, comparing of TETact-v3 cells targeting CD4 promoter to with cells expressing non-targeting sgRNA revealed CD4 as the sole significantly upregulated gene. Expression of the other genes in the CD4-targeting samples correlated strongly with the control sample. Together these experiments reveal the exquisite specificity of the TETact system.

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Two biological replicates were prepared of wild-type A20 cells, A20 cells with CD4 activators and A20 cells with non-targeting activators. RNA-seq and whole genome methyl-seq profiles were prepared of all six samples.

Refer to individual Series
 
Citation(s) 36151095
Submission date Aug 30, 2022
Last update date Oct 26, 2022
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platforms (1)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (12)
GSM6160901 Wild-type A20 replicate 1
GSM6160902 Wild-type A20 replicate 2
GSM6160903 A20 with sgRNA activating CD4 gene replicate 1
This SuperSeries is composed of the following SubSeries:
GSE203162 RNA-seq of A20 mouse cells using a novel TETact activation of CD4
GSE211754 Whole genome enzymatic methyl-seq of A20 mouse cells using a novel TETact activation of CD4
Relations
BioProject PRJNA875089

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Supplementary file Size Download File type/resource
GSE212345_RAW.tar 1.2 Gb (http)(custom) TAR (of COV, TSV)
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