title: RNA-seq differential expression studies: more sequence or more replication?
abstract: BACKGROUND
  RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources.
  
  
  RESULTS
  We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. In the human cell line MCF7, adding more sequencing depth after 10 M reads gives diminishing returns on power to detect DE genes, whereas adding biological replicates improves power significantly regardless of sequencing depth. We also propose a cost-effectiveness metric for guiding the design of large-scale RNA-seq DE studies. Our analysis showed that sequencing less reads and performing more biological replication is an effective strategy to increase power and accuracy in large-scale differential expression RNA-seq studies, and provided new insights into efficient experiment design of RNA-seq studies.
  
  
  METHODS
  The code used in this paper is provided on: http://home.uchicago.edu/∼jiezhou/replication/. The expression data is deposited in the Gene Expression Omnibus under the accession ID GSE51403.
authors: Institute of Genomics and Systems Biology, Committee on Development, Regeneration, and Stem Cell Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
authors: Yuwen
authors: Y
authors: Liu
authors: Jie
authors: J
authors: Zhou
authors: Kevin P
authors: KP
authors: White
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D061986:MCF-7 Cells; D015203:Reproducibility of Results; D018401:Sample Size; D017423:Sequence Analysis, RNA / Q000379:methods*