Progenies from heterozygous dscaml1 mutant parents were anesthetized and harvested at 3.5-4 dpf. The anterior half of the animal was used for RNA preparation using the RNA Miniprep Kit (Zymo). The posterior half was used for genotyping. Three biological replicates for each group were analyzed, each containing RNA from 6–11 animals. All samples had RIN ≥8.0 and were converted into a strand-specific library using Illumina’s TruSeq Stranded mRNA HT Sample Prep Kit (RS-122–2,103; Illumina) for subsequent cluster generation and sequencing on Illumina’s NextSeq 75 sequencer. Sequence data processing, alignment, read count, mapping, and quality control were performed as previously described (Ates et al., 2020 (link)). Differential expression was tested for significance using the false discovery rate (FDR) (Benjamini–Hochberg) corrected Likelihood Ratio Test (LRT) in the R-package DESeq2 (Love et al., 2014 (link)). 238 and 116 genes showed a significant difference in read counts at FDR < 0.01 and 0.001, respectively. Original sequence data have been deposited in NCBI’s Gene Expression Omnibus (Edgar et al., 2002 (link)) and accessible through GEO Series accession number GSE213858.
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