Gene expression profiling of the Arabidopsis glucosinolate deficient mutants, ref5-1 and ref2-1 and med5 mutants

Purpose: To identify changes in gene expression in ref5-1 and ref2-1 compared with wild type and ref5-1 med5 and ref2-1 med5 compared to ref5-1 or ref2-1 respectively Methods: Gene expression profiles were generated from 18-day-old, pooled Arabidopsis rosettes in biological quadruplicate, by paired-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR. Results: We identified 71 genes that were differentially expressed in both ref5-1 and ref2-1 compared to wild type but their altered expression is restored. Overall design: Gene expression profiles of wild type and mutants were generated in biological triplicate from 18-day-old Arabidopsis rosettes by deep sequencing using Illumina HiSeq 2500.

研究目的：旨在鉴定ref5-1与ref2-1相较于野生型的基因表达变化，以及ref5-1 med5、ref2-1 med5分别相较于ref5-1、ref2-1的基因表达变化。
实验方法：以生长18天的拟南芥莲座叶为材料，进行四次生物学重复混合取样，采用Illumina HiSeq 2500平台对100 bp片段开展双端测序，以生成基因表达谱。将通过质量过滤的序列读段比对至TAIR10参考基因组，比对工具为TopHat。使用HTseq-count进行基因计数，借助edgeR完成差异表达分析。
实验结果：本研究鉴定出71个基因，在ref5-1与ref2-1相较于野生型时均呈现差异表达，且其表达改变可被恢复。
整体实验设计：以生长18天的拟南芥莲座叶为材料，进行三次生物学重复，采用Illumina HiSeq 2500平台开展深度测序，以生成野生型及突变体的基因表达谱。