Gene expression profiling of Huh7 and THP1 cells after siRNA knockdown of C5/TRAF1 intergenic transcript

The C5/TRAF1 locus is a well validated genetic risk factor for RA. Upon further investigation of this region we recently discovered that the intergenic region between these two immune-related genes is activelly transcribed in a variety of tissues and is up-regulated in PBMCs, monocytes, B- and T-cells upon immune stimulation. The present study aimed to characterize the biological function of this newly identified C5/TRAF1 intergenic transcript, by analysing the effect of its knockdow on the gene expression profiles of Huh7 and THP1 cells. siRNA transfections with the intergenic specific siRNA and 2 negative control siRNAs were performed in duplo and independently repeated 4 times per cell line, with different cell culture passages to account for the biological variation. The 4 independent experiments per cell line were divided in two design phases: the Discovery Phase (experiments 1 and 2) and the Validation Phase (experiments 3 and 4).