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Specifications


Application: Gene expression microarray analysis
Number of samples: 21
Release date: Apr 28 2016
Last update date: Aug 9 2018
Access: Public
Diseases: Lung Neoplasms, Neoplasms
Dataset link Effect of APE1 and its acetylation on gene expression profile of lung cancer cells

Experimental Protocol


We used two different sets of experiments. In one set we used lung adenocarcinoma A549 cells and determined the gene expression profile of control (control siRNA transfected) and APE1-downregulated (APE1 siRNA transfected) A549 cells. Additionally, to examine the effect of acetylation of APE1, we used trichostatin A (TSA; which increases APE1's acetylation) and treated both control and APE1-downregulated cells with TSA (100 ng/ml) for 4 hrs. We compared the gene expression profile between (i) control vs. APE1 siRNA cells (this analysis will determine the genes whose expression is affected by APE1), and also between (ii) TSA-treated control vs. TSA-treated APE1 siRNA cells (this analysis will determine the genes whose expression is specifically affected by APE1's acetylation). In another set we used normal bronchial epithelial BEAS-2B cells. In these cells we overexpressed wild type (WT) APE1 (that can be acetylated), K6R/K7R (RR) mutant APE1 (that cannot be acetylated) or N-terminal 42 amino acid deleted (ND42) mutant APE1 (that lacks the N-terminal domain of APE1 which harbors the acetylation sites). We compared the gene expression profile between (i) WT vs. RR (this analysis will determine the genes whose expression is affected by acetylable APE1), and between (ii) WT vs. ND42 (this this analysis will determine the genes whose expression is affected by full-length acetylable APE1). We have 3 biological replicates for each sample designated as 1, 2, 3 (equivalent to a,b,c).

Repositories


GEO

GSE74572

BioProject

PRJNA300854

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Contact


Shiladitya Sengupta

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