Fig. 3

Validation of gene expression changes estimated with CANEapp with quantitative real-time PCR. a RNA-seq analysis of hippocampi of Alzheimer’s disease patients and controls. Hippocampal tissue from 4 AD patients and 4 control individuals was used to extract total RNA and perform ribodepletion and strand-specific library preparation. Single-end RNA sequencing was performed on Illumina HiSeq 2000. Fold changes of expression for 2 downregulated and 4 upregulated genes measured with real-time PCR was compared with expression values generated by CANEapp. b RNA-seq of developing mouse cortex. Tissue from 4 embryonic day 17 and 3 adult mouse cortical samples was processed to extract polyA-selected RNA and generate paired-end unidirectional sequencing data with Illumina Genome Analyzer IIx. Gene expression estimates of 4 downregulated and 4 upregulated genes were compared between CANEapp and real-time PCR. c Fold changes of gene expression for RNA-seq of liver of rats treated with two DNA-damage compounds. The data was produced by paired-end sequencing of polyA-selected RNA on Illumina HiSeq 2000. Fold changes of expression for 2 downregulated and 4 upregulated genes were compared between CANEapp and real-time PCR. R²-coefficient of determination