Messenger RNA transcriptome data from wild-type zebrafish (Danio rerio) larvae after chemical-induced seizure using pentylenetetrazole (PTZ).. Three different conditions were investigated: (i) status epilepticus, SE (3h of PTZ-induced seizure); (ii) acute seizure, AC (20 minutes of PTZ-induced seizure); and (ii) a SE control group (no PTZ exposure). The study was carried out by high-throughput sequencing, using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) followed by sequencing by Illumina Hi-Seq 2500 (Illumina, San Diego, CA, USA).