Transcriptomic Analysis of nckap1l Mutant

Total RNA from 20 wild-type siblings and 20 nckap1l^lri35 mutant larvae was collected at 5 dpf using the Qiagen RNeasy mini kit (Qiagen, Cat. 74104) according to the manufacturer’s instructions. cDNA for next-generation sequencing was synthesized by using the TruSeq standard total RNA kit (Illumina, 20020598) according to the manufacturer’s instructions. Using an Illumina HighSeq 2500, a total of 11.5 and 10.5 millions of paired-end 50-bp reads were obtained from wild-type and mutant cDNA, respectively. Raw reads were aligned to the zebrafish genome (GRCz10) using TopHat [27 (link)]. The lri35 mutation was mapped to chromosome 11 by MMAPPR [24 (link)]. The NGS and analyzed data are available in the GEO repository at the NCBI (GSE153386).