Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Sirt6-/- mTEC Transcriptomes

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods:mTECl mRNA profiles of 4 weeks old wild-type (WT) and sirtuin 6 knockout (Sirt6-/-) mice were generated by deep sequencing using Illumina HiSeq 3000. Conclusions: Our study revealed that the expression of epigenetic regulator Sirt6 in TECs is crucial for the development and differentiation of mTECs and for the induction of central immune tolerance. Sirt6 deficiency leads to reduced DNA replication and impaired proliferation of mTECs, and specifically accelerates the differentiation of mTECs from CD80-Aire- immature population to CD80+Aire- intermediate mature population by promoting the expression of Spib. mTEC mRNA profiles of 4 weeks old wild type (WT) and Sirt6-/- mice