Analysis of the expression of Ataxin-2-target genes

We recently identified the RNA targets of Ataxin-2 by using PAR-CLIP. To elucidate the functional role of Ataxin-2 on target-binding, we have knocked down or overexpressed Ataxin-2 in HEK293T cells and extracted RNAs 48 hrs after transfection. Then, these total RNAs were subjected to whole transcripts microarray analysis to examine how the perturbation of Ataxin-2 expression affects target gene expression. Ataxin-2 was either knocked down using siRNA or overexpressed using the expression construct of Halo-Ataxin-2.Control siRNA was transfected as a control of knockdown experiment. The expression construct of Halo-tag alone was used as a control of overexpression experiment. Forty-eight hrs after transfection, total RNAs were extracted and subjected to microarray analysis.