@article{b420687b37a140a384d55572aa4e4d2d,
title = "RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method",
abstract = "Peripheral blood is a highly accessible biofluid providing a rich source of information about human physiology and health status. However, for studies of the blood transcriptome with RNA sequencing (RNA-Seq) techniques, high levels of hemoglobin mRNAs (hgbRNA) present in blood can occupy valuable sequencing space, impacting detection and quantification of non-hgbRNAs. In this study, we evaluated two methods for preparing ribosomal RNA (rRNA)-depleted sequencing libraries for RNA-Seq of whole blood, one of which is also designed to deplete hgbRNAs. Two experiments were performed: one evaluating library performance across 6 human blood samples and the other examining library reproducibility and performance in a two-subject subset. We find that addition of hgbRNA depletion to the rRNA-depletion protocol for library preparation from blood RNA effectively reduces highly abundant hgbRNA reads; however, it does not result in a statistically significant increase in differentially expressed genes in our patient-control study. Bioinformatic removal of globin gene counts in non-hgbRNA depleted libraries provides improvement in overall performance of these libraries. We conclude that use of a standard ribosomal RNA depletion method for library preparation coupled with bioinformatic removal of globin gene counts is sufficient for reproducible and sensitive measurement of both coding and noncoding RNAs in the blood transcriptome.",
author = "Harrington, {Christina A.} and Fei, {Suzanne S.} and Jessica Minnier and Lucia Carbone and Robert Searles and Davis, {Brett A.} and Kimberly Ogle and Planck, {Stephen R.} and Rosenbaum, {James T.} and Dongseok Choi",
note = "Funding Information: RNA isolation was performed in the OHSU Gene Profiling Shared Resource. Library preparation and short read sequencing assays were performed in the OHSU Massively Parallel Sequencing Shared Resource under the direction of Robert Searles. RNA-Seq data processing was performed in the Oregon National Primate Research Center{\textquoteright}s Bioinformatics & Biostatistics Core. We thank Kristina Vartanian and Amy Carlos for excellent technical assistance. We are grateful to Christina Zheng for helpful discussion regarding RNA-Seq alignment and Q.C., to Karina Ray for assistance with data deposition, and Katinka Vigh-Conrad for assistance with figures. This work was enabled in part by the OHSU Exacloud computational environment developed in partnership with Intel and operated by the OHSU Advanced Computing Center. This study was funded by NIH Grants R01EY026572, RO1EY020249 and P30EY010572 and by a Research to Prevent Blindness award to the Casey Eye Institute. J.T.R. receives support from the William and Mary Bauman Foundation, the Stan and Madelle Rosenfeld Family Trust, and the Grandmaison Fund for Autoimmunity Research. The Gene Profiling Shared Resource and Massively Parallel Sequencing Shared Resource receive support from the OHSU Knight Cancer Institute NCI Cancer Center Support Grant P30CA069533. The Oregon National Primate Research Center{\textquoteright}s Bioinformatics & Biostatistics Core is funded in part by the center{\textquoteright}s core grant: NIH/OD P51 OD011092. Publisher Copyright: {\textcopyright} 2020, The Author(s).",
year = "2020",
month = dec,
day = "1",
doi = "10.1038/s41598-020-62801-6",
language = "English (US)",
volume = "10",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",
}