Journal article

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie

NUCLEIC ACIDS RESEARCH | OXFORD UNIV PRESS | Published : 2017

Abstract

Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples. The systematic gene expression changes induced by this design allowed benchmarking of different library preparation kits (st..

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Grants

Awarded by NationalHealth and Medical Research Council


Awarded by NATIONAL CANCER INSTITUTE


Funding Acknowledgements

National Health and Medical Research Council [1050661 to M.E.R., G.K.S. and M.L.A.L., 1079756 to M.L.A.L. and M.E.R., 1045936 to M.E.R. and 1059622 to M.E.R., Fellowships 1104924 to M.E.R. and 1058892 to G.K.S.]; Victorian State Government Operational Infrastructure Support, Australian Government NHMRC IRIISS and the Ian Potter Centre for Genomics and Personalised Medicine.