Transcriptomic Analysis of Anxiety-like Behavior in Zebrafish

We further carried out a transcriptomic analysis of brain samples from a publicly available dataset (accession number GSE61108) of adult zebrafish with different inherent levels of anxiety-like behavior. The strains in the dataset included AB (also used in the above experiments), which is a low anxiety-like strain, common in laboratories, and two other strains with higher anxiety-like behavior, termed here collectively as SB, comprising LSB (low stationary behavior) and HSB (high stationary behavior) [71 (link),72 (link)]. Each strain was represented by four pooled samples of ten whole brains (two males and two females); thus, for our analysis, there were four AB samples and eight SB samples (four HSB and four LSB). cDNA libraries had been generated with TruSeq RNA Sample Prep V2 of Illumina and sequenced as 72 bp single ends on Illumina (GA_IIX), similar to our procedures. To analyze this dataset, we used a similar procedure to the RNA analysis for larval samples, with one exception. FastQC, version v0.11.9 revealed TruSeq adapters, which we removed with Trimmomatic v.0.36 and further confirmed removal by FastQC analysis. The remaining analysis was executed with RSEM and DESeq2, as described above.