Fig. 2

The workflow of RNA-seq data analysis. a Main steps and bioinformatics tools used in the study. The programs for data analysis were shown in colored boxes and the software packages in transparent boxes. b Principal component analysis (PCA) of gene expression profiles for four different groups. The distance between the groups indicates the variance. The colored dots represent data replicates within the same group: purple for the control (Ctrl) of Songpu mirror carp, blue for the cold acclimation (CA) of Songpu mirror carp, green for the control (Ctrl) of Barbless carp, red for the cold acclimation (CA) of Barbless carp. c Validation of RNA-seq data using qPCR. Log2 Fold changes of RNA-seq data for gene expression were plotted against those of qPCR data. The reference line in red indicates the linear relationship between the results of RNA-Seq and qPCR