Global transcriptomic response to chilling temperature in Col-0 wild type and sig5-3 (SALK_141383C) mutant Arabidopsis plants.

Purpose: Investigate whether a nuclear-encoded sigma factor (SIGMA FACTOR5, SIG5; controls chloroplast transcription) regulates the transcriptome (RNA-seq) in response to chilling. Overall design: Col-0 wild type and sig5-3 seedlings were grown under light/dark cycles for 11 days and exposed to continuous light for 24 h before start of experiment. After 24 h under continuous light, one set of seedlings was exposed to 5 h chilling (4 °C), commencing at ZT27, and the other set was exposed to 3 h of chilling, commencing at ZT45. Both sets of chilled samples had parallel controls that were not chilled (19 °C). Each treatment had 3 independent replicates. Total RNA was extracted and RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Sequencing was performed using an Illumina NextSeq 500 using NSQ 500 Hi-Output kit v2 (150 cycle). Sequence data were imported into Partek Genomics Suite version 6.6 (Partek, St. Louis, 385 MO, USA), further trimmed and aligned to the Arabidopsis thaliana genome (TAIR11) using STAR (version 2.4.1d). Genes with a fold change of |log2| > 1.5 and a false detection rate of < 0.05 were considered as differentially-expressed.