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Table 3 Description of datasets used to validate CANEapp performance to estimate differential gene expression

From: CANEapp: a user-friendly application for automated next generation transcriptomic data analysis

Name Organism Experimental groups N of samples RNA selection protocol Library preparation Single or paired-end GEO
Transcriptomic changes in hippocampi of Alzheimer’s disease patients Homo sapiens Alzheimer’s disease vs age- and sex-matched neurologically normal controls 4 vs 4 Ribo-depletion Illumina directional small RNA prep single GSE67333
Transcriptomic changes in embryonic and adult mouse cortex Mus musculus E17 cortex vs adult cortex 4 vs 3 Poly-A selection Illumina mRNA-Seq prep paired GSE39866
SEQC Rat liver toxicogenomics study Rattus norvegicus N-Nitrosodimethylamine, Aflatoxin B1 vs Vehicle treatments 3 vs 3 Poly-A selection Illumina TruSeq RNA paired GSE55347
3 vs 4