Boudichevskaia Anastassia, Cao Hieu Xuan, Schmidt Renate
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466, Stadt Seeland, Germany.
Plant Cell Rep. 2017 Aug;36(8):1323-1332. doi: 10.1007/s00299-017-2157-5. Epub 2017 May 22.
Excluding polymorphic probes from GeneChip transcript profiling experiments via a sequence-based approach results in improved detection of differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24. GeneChip arrays represent a powerful tool for transcript profiling experiments. The ATH1 GeneChip has been designed based on the sequence of the Arabidopsis thaliana reference genome Col-0, hence the features on the array exactly match the sequences of Col-0 transcripts. In contrast, transcripts of other A. thaliana accessions or related species may show nucleotide differences and/or insertions/deletions when compared to the corresponding Col-0 transcripts, therefore, comparisons of transcript abundance involving different A. thaliana accessions or related species may be compromised for a certain number of transcripts. To tackle this limitation, a sequence-based strategy was developed. Only features on the array that were identical in sequence for the specimen to be compared were considered for transcript profiling. The impact of the proposed strategy was evaluated for transcript profiles that were established for developing seeds of A. thaliana accessions Col-0 and C24.
通过基于序列的方法从基因芯片转录本分析实验中排除多态性探针，可提高对拟南芥Col-0和C24品系发育种子中差异表达基因的检测。基因芯片阵列是转录本分析实验的强大工具。ATH1基因芯片是根据拟南芥参考基因组Col-0的序列设计的，因此阵列上的特征与Col-0转录本的序列完全匹配。相比之下，其他拟南芥品系或相关物种的转录本与相应的Col-0转录本相比，可能会出现核苷酸差异和/或插入/缺失，因此，涉及不同拟南芥品系或相关物种的转录本丰度比较可能会因一定数量的转录本而受到影响。为了解决这一限制，开发了一种基于序列的策略。在转录本分析中，仅考虑与待比较样本序列相同的阵列特征。针对为拟南芥Col-0和C24品系发育种子建立的转录本图谱，评估了所提出策略的影响。
