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. Isolated 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 characterized and identified genes involved in dedifferentiation of islets. 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.研究目的：本数据集旨在对比分析2型糖尿病db/db小鼠胰岛去分化过程中涉及的基因表达谱。 实验方法：选取12周龄小鼠，通过灌流法分离纯化野生型（Wild Type，WT）、db/+及db/db小鼠的胰岛，提取总RNA后开展RNA测序（RNA seq），以解析其基因表达模式。 实验结果：采用优化的数据分析流程，将每个样本约1000万条序列读数比对至小鼠基因组（mm9组装版本），通过TopHat分析流程在野生型、db/+及db/db小鼠的胰岛中共鉴定到16014个转录本。对差异表达基因进行层级聚类分析，揭示了其在2型糖尿病中的作用。基于TopHat流程的数据分析结果显示，转录组分析虽存在显著的结果重叠，但也提供了互补的研究视角。 研究结论：本研究表征并鉴定了参与胰岛去分化过程的相关基因。本数据集采用Illumina Hiseq 2500测序平台，对12周龄野生型（WT）、db/+及db/db小鼠的胰岛mRNA进行了三次生物学重复的深度测序。