Influence of RNA extraction methods and library selection schemes on RNA-seq data.

ABSTRACT:

Background

Gene expression analysis by RNA sequencing is now widely used in a number of applications surveying the whole transcriptomes of cells and tissues. The recent introduction of ribosomal RNA depletion protocols, such as RiboZero, has extended the view of the polyadenylated transcriptome to the poly(A)- fraction of the RNA. However, substantial amounts of intronic transcriptional activity has been reported in RiboZero protocols, raising issues regarding their potential nuclear origin and the impact on the actual sequence depth in exonic regions.

Results

Using HEK293 human cells as source material, we assessed here the impact of the two commonly used RNA extraction methods and of the library construction protocols (rRNA depletion versus mRNA) on 1) the relative abundan

SUBMITTER: Sultan M 

PROVIDER: S-EPMC4148917 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature