RNA-seq of 10-day-old Arabidopsis seedlings of Col-0, cpl3 mutant, and pentuple-della mutant genotype

C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3) is a phosphatase that interacts with the DELLA proteins RGA and GAI, promoting their function. We examined whether CPL3 is involved in regulating the activity of DELLAs, in particular regarding their function in controlling gene expression. For this purpose, we profiled the transcriptome of the cpl3-3 mutant and compared it with that of the dellap (pentuple della) mutant in the same conditions. 10-day-old plants were used to extract RNA with the miRNeasy Mini Kit (Qiagen). The RNAs were first selected via enrichment of their poly(A) tail and then further fragmented into 300~350 bp fragments to build the libraries. Then, the libraries were sequenced on BGIseq500 platform (BGI, Shenzhen, China), the raw data of FASTQ format were firstly processed through in-house Perl scripts. Next, clean reads were aligned to the Arabidopsis reference genome (TAIR10) using HISAT2. StringTie2 was used to count the reads numbers mapped to each gene and the R package DESeq2was used for differential expression analysis. The principal component analysis (PCA) and Pearson correlation were analyzed by the in-house R Script. All experiments were performed in three biological replicates.