Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

Table 1 RNA-Seq data sets

Experiment	1	2	3	4
Species	Mus musculus	Mus musculus	Homo sapiens	Homo sapiens
Sample	Lip tissue	Keratinocytes (primary)	Hematopoietic cells (primary)	NuLi cells (cell line)
Control group (n)	3	3	3	3
Treated group (n)	3	3	3	3
Platform	Illumina HiSeq2000	Illumina NextSeq	Illumina NextSeq	Illumina NextSeq
Reads PE^a (average^d)	35.3 M	37.4 M	84.7 M	37.2 M
Reads SE^b (average^d)	35.0 M	38.2 M	85.3 M	37.5 M
Reads NS^c (average^d)		37.5 M	84.9 M	37.3 M

^aPE, paired-end reads
^bSE, single-end reads
^cNS, non-strand specific protocol for the paired-end reads
^dTotal number of reads from featureCounts summary (assigned plus non-assigned) with average of totals taken over the six samples in each experiment

ISSN: 1471-2164