RNA-seq to compare wild type, db/+ and db/db islets

Purpose: RNA seq analysis were to compare and contrast the gene expression profile involved in the dedifferentiation of db/db islets in type 2 diabetes Methods: Islets of wild type, db/+ and db/db were purified using perfusion from 12 week old mice and RNA were isolated. Islated RNA were used in RNA seq to understand the expression pattern Results: Using an optimized data analysis workflow, we mapped about 10 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts WT, db/+ and db/db mice islets with TopHat workflow. Hierarchical clustering of differentially expressed genes uncovered there role in type 2 diabetes. Data analysis with TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: We characterised and identified genes involved in dedifferentiation of islets. Overall design: Islets of mRNA 12 weeks old wild type (WT), db/+ and db/db mice were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.

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Neelankal John A, Ram R, Jiang FX