Quantitative Analysis of Neurog2 Heterozygote, Mutant and and Mash1KI Retinal Transcriptomes by RNA Sequencing

To generate an unbiased view of changes to the retinal gene network in Neurog2 retinal mutants as well as understanding the effects of Mash1 ectopic expression in a Neurog2 retinal mutant, we generated and compared the E12.5 transcriptomes from Neurog2 heterozygote, Neurog2 mutant and Neurog2 mutant;Mash1 knock-in mice. A pair of E12.5 retinas from each biologic replicate underwent FACS sorting to isolate GFP+ cells. GFP+ cells were used to produce libraries for high throughput sequencing (n = 3 biologic replicates/genotype). Reads were aligned with BWA and Bowtie programs to the mm10 genome. Aligned reads were then analyzed for differentially expressed transcripts using the CuffDiff program in the Galaxy online bioinformatics package (www.usegalaxy.org). Total RNA from Neurog2GFP/+(heterozygote; n = 3), Neurog2GFP/GFP(mutant; n = 3), and Neurog2GFP/Mash1KI(Mash1 knock-in; n = 3) E12.5 retinas.