Transcriptome sequencing analysis of SH-SY5Y cells infected with EV71 reveals the potential neuropathic mechanisms.

•We found a profile of dysregulated transcriptomes in SH-SY5Y cells with EV71 infection.•A total of 82,406,974, 112,410,808 and 87,780,371 clean reads were found in the Control, EV71-12 h and EV71-24 h groups, respectively.•The results showed that the enriched GO term “Nervous system development” and enriched pathway “CCKR signaling map” might be important contributors to EV71-induced neuropathological mechanism.