title: RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library.
abstract: The most popular RNA library used for RNA sequencing is the poly(A) captured RNA library. This library captures RNA based on the presence of poly(A) tails at the 3' end. Another type of RNA library for RNA sequencing is the total RNA library which differs from the poly(A) library by capture method and price. The total RNA library costs more and its capture of RNA is not dependent on the presence of poly(A) tails. In practice, only ribosomal RNAs and small RNAs are washed out in the total RNA library preparation. To evaluate the ability of detecting RNA for both RNA libraries we designed a study using RNA sequencing data of the same two breast cancer cell lines from both RNA libraries. We found that the RNA expression values captured by both RNA libraries were highly correlated. However, the number of RNAs captured was significantly higher for the total RNA library. Furthermore, we identify several subsets of protein coding RNAs that were not captured efficiently by the poly(A) library. One of the most noticeable is the histone-encode genes, which lack the poly(A) tail.
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Shilin
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Quanhu
authors.initials: Q
authors.lastname: Sheng
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Mingsheng
authors.initials: M
authors.lastname: Guo
authors.affiliation: Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Lehmann
authors.affiliation: Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Pietenpol
authors.affiliation: Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Samuels
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shyr
mesh_terms: D020869:Gene Expression Profiling; D015723:Gene Library; D006801:Humans; D016366:Open Reading Frames / Q000235:genetics; D011061:Poly A / Q000235:genetics*; D012313:RNA / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D012335:RNA, Ribosomal; D011061:Poly A; D012313:RNA