Figure 2

Feasibility and setup of xenoarray analysis. (A) Cross-species BLAST analysis for 50-mer probes from Illumina Mouse Whole Genome chip V1, against transcriptome databases for murine, human and canine transcripts. The best match for each probe was chosen as the BLAST hit with the highest number of identical nucleotides and the lowest e-value for significance. The histogram shows the distribution of the number of identical nucleotides between the probes and their best hits, respectively in the Murine, Canine and Human transcriptomes, as indicated. (B, C) Xenoarray analysis on untransduced and library-transduced HeLa cells (MOI ~1.25) using the T7-dT primer (B) or the T7-pFB primer (C). In these dot plots, each dot represents a probe signal, the coordinates of which are given by the intensity in the untransduced (x-axis) and in the transduced (y-axis) cell samples. Murine transcripts, specifically detected by the murine microarray only in the transduced cells, are highlighted by a continuous red circles. Endogenous human transcripts, giving cross-hybridization signals in both samples, are highlighted by a dotted red circle. (D) Numbers of probes giving significant signal using T7-dT or T7-pFB primers for Xenoarray analysis on HeLa cells transduced with the retroviral library at different MOI, from 0 (CTRL) to 5, as indicated.