Study : Gene expression profiling study by RNA-seq in Arabidopsis thaliana treated with Chlorella
Gene expression profiling study by RNA-seq in Arabidopsis thaliana treated with Chlorella
The objective of this study is to assess gene expression changes in Arabidopsis thaliana after Chlorella treatment. We performed transcript profiling using 4 RNA-seq samples of Arabidopsis obtained at 0h and 12h after Cholorella treatment. To compare them with control sample groups, 6 RNA-seq samples treated with additional DC3000 pathogen or only water were generated. Through various statistical tests, differentially expressed genes at each time point were obtained and enriched biological functions were compared between treatment time points. Many enriched functions associated with immune or defence systems of plant were common in all treatment times. Overall design: RNA-seq data of 10 samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturers protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).