Impact of library preparation on downstream analysis and interpretation of RNA-seq data: comparison between Illumina PolyA and NuGEN Ovation protocol

ABSTRACT: Objectives: The sequencing by the PolyA selection is the most common approach for library preparation. With limited amount or degraded RNA, alternative protocols such as the NuGEN have been developed. However, it is not yet clear how the different library preparations affect the downstream analyses of the broad applications of RNA sequencing. Methods and Materials: Eight human mammary epithelial cell (HMEC) lines with high quality RNA were sequenced by Illumina’s mRNA-Seq PolyA selection and NuGEN ENCORE library preparation. The following analyses and comparisons were conducted: 1) the numbers of genes captured by each protocol; 2) the impact of protocols on differentially expressed gene detection between biological replicates; 3) expressed single nucleotide variant (SNV) detection; 4) non

ORGANISM(S): Homo sapiens

SUBMITTER: Zhifu Sun 

PROVIDER: E-GEOD-47933 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress