Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.

ABSTRACT: Next-generation sequencing is excellently suited to evaluate the abundance of mRNAs to study gene expression. Here we compare two alternative technologies, cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE), for the same RNA samples. Along with quantifying gene expression levels, CAGE can be used to identify tissue-specific transcription start sites, while SAGE monitors 3'-end usage. We used both methods to get more insight into the transcriptional control of myogenesis, studying differential gene expression in differentiated and proliferating C2C12 myoblast cells with statistical evaluation of reproducibility and differential gene expression. Both CAGE and SAGE provided highly reproducible data (Pearson's correlations >0.92 among biological triplicates).

SUBMITTER: Hestand MS 

PROVIDER: S-EPMC2938216 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature