Transcriptomic analysis of the effect of PFOS in Arabidopsis.
To determine the mechanism by which A. thaliana responds to PFOS, we performed an RNA-seq experiment to identify transcriptome changes at the genome-wide level. We aimed to examine early differentially expressed genes in order to understand how PFOS may be taken up by the plant and which metabolic pathways facilitate the plant to sense and respond to PFOS.RNA was isolated from WT (Col-0) plants that had been grown 10 days in 0 ppm PFOS before PFOS treatment plants were transferred to sterile water for 1 days. Water was replaced by 20 mg/L PFOS for 3 or 6 hr. Ten seedlings were pooled for each biological replicate, and three biological replicates per treatment were sequenced. Seedlings were ground in liquid nitrogen and RNA was isolated using the Spectrum Total RNA Extraction Kit (Sigma Aldrich). 150 bp paired end reads were sequenced. Reads were trimmed, mapped, and expression was normalized using the program Salmon. Reads were mapped to the TAIR10 genome release of Arabidopsis thaliana. Differential expression of RNA-seq reads was analyzed using DEseq2 (version 3.13), and p-values were adjusted using the False Discovery Rate approach. Significant differentially expressed genes compared to control plants were determined by an adjusted p-value <0.05 and a log2 fold change of > 1 .