RNAseq of partially paralyzed zebrafish embryos at 5 days post-fertilization compared to normal siblings

Sofa potato (sop) is a mutant zebrafish line, whose synaptic transmission at the neuromuscular junction is absent due to a point mutation in the δ subunit gene of the acetylcholine receptor (AChR), leading to paralysis of its skeletal muscles (doi:10.1523/jneurosci.0851-04.2004). To explore genetic changes in synapses caused by the lack of synaptic transmission, we performed RNA-seq analysis of normal siblings (sop+/?) and sop homozygous embryos (sop-/-) at 5 dpf. Sop-/- had an inducible wild type δ subunit gene, which was induced at 2 dpf resulting in partial paralysis (doi:10.1038/s41598-017-01900-3). Zebrafish embryos obtained from a cross of sop+/- were separated into the paralyzed homozygous group (sop-/-) and the swimming siblings (sop+/+ or sop+/-). Both groups were subjected to mifepristone to induce wild type delta subunit to partially rescue paralyzed fish. Total RNA was extracted from both groups (~10 larvae in each) at 5 dpf using RNeasy Mini Kit (QIAGEN). Next-Generation sequencing and bioinformatics analysis was performed using TopHat and Cufflinks by Zymo Research. Read counts were ~56M and ~144M for sop-/- and controls respectively.