Future experiments could use this EDGE and paired analysis technique to test cDNA sequences generated from younger, possibly neonatal, mice in order to determine if the striped pattern forms due to differential gene expression earlier in development. This would be aided by the development of a high quality reference genome for the striped mouse and would allow additional relevant genes to be detected, as samples could be compared to the reference genome instead of being compared to Mus musculus.
References Hong LZ, Li J, Schmidt-Küntzel A, Warren WC, Barsh GS. Digital gene expression for non-model organisms. Genome Res. 2011 Nov;21(11):1905-15. Epub 2011 Aug 15.
B
Figure 1. A. The striped mouse, Rhabdomys pumilio. B. The striped pattern can be viewed from the mouse’s dorsal side. Naming convention designates the white dorsal midline as DrW, the dorsal-most black stripe as BlA, the white stripe that follows as Wh, and the ventral-most black stripe as BlB.
Figure 2. Unpaired analysis of the striped mouse gene counts resulted in fewer genes with low False Discovery Rates. This was consistent in every comparison. Each point represents one gene that was expressed in the sample The “Number called” axes refer to the number of times the gene was detected in each sample.
Figure 3. In the paired analyses, the number of genes with low FDRs varies with each comparison. The analysis of BlA vs. BlB yielded the most low-FDR (differentially expressed) genes.
30 • inquiro | no. 6 | 2012