Transcriptome analysis of Arabidopsis Root in response to cellooligomers (cellotriose)

Purpose: We recently identified a mutant (cork1) which did not respond to cellooligomers (COs). To find out the signaling events following CO perception, roots from the segregated wild-type and homozygous mutants (F2 generation from cork1-2 X AeqWT) were treated with 10 µM cellotriose and water. Total RNA from root tissue was extracted after 1 hour. The raw reads were mapped to TAIR10 reference genome with STAR (v. 2.7.10a). Readcounts were generated from the mapped bam files with featureCount (v. 2.0.1). DESeq2 (v. 1.34.0) was applied to calculate the fold change and statistics for each mapped gene. Roots from 8 seedlings of segregated wid-type or homozygous mutant were treated with 1mL of water or 10 µM cellotriose. Root tissues were collected after 1 hour for total RNA extraction. For each sample, 16 seedlings were used.