Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing
Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing
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DOI：
10.1016/j.jbiotec.2011.09.014
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发表时间：
2011-12-10
影响因子：
4.1
通讯作者：
Brinkrolf, Karina
中科院分区：
文献类型：
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作者：
Becker, Jennifer;Hackl, Matthias;Brinkrolf, Karina
来自454 Life Sciences的焦磷酸测序技术和使用Newbler Assembler的cDNA序列的新组装方法被用于实现解开中国仓鼠卵巢（CHO）细胞的转录组的重大进步。对来源于几种细胞系和不同培养条件的标准化cDNA文库进行测序，并将所得的184万个读段组装成32，801个连续序列、29，184个同种组和24，576个同种组。分类学分类的isotig表明，超过70%的组装数据是最相似的小家鼠的转录组，其余的isotig大部分同源的DNA序列从褐家鼠。CHO细胞系重叠群到小鼠转录组的作图表明，代表6701个基因的9124个小鼠转录本被其序列长度的95%以上覆盖。从转录组数据重建了中心碳水化合物代谢的代谢途径和用于蛋白质N-糖基化的糖的生物合成途径。检测代表CHO细胞N-糖基化途径中主要步骤的所有相关基因。目前的手稿代表了一个数据集的组装和注释的基因CHO细胞，现在可以用于详细分析CHO细胞系的分子功能。(C)2011爱思唯尔有限公司版权所有。
The pyrosequencing technology from 454 Life Sciences and a novel assembly approach for cDNA sequences with the Newbler Assembler were used to achieve a major step forward to unravel the transcriptome of Chinese hamster ovary (CHO) cells. Normalized cDNA libraries originating from several cell lines and diverse culture conditions were sequenced and the resulting 1.84 million reads were assembled into 32,801 contiguous sequences, 29,184 isotigs, and 24,576 isogroups. A taxonomic classification of the isotigs showed that more than 70% of the assembled data is most similar to the transcriptome of Mus musculus, with most of the remaining isotigs being homologous to DNA sequences from Rattus norvegicus. Mapping of the CHO cell line contigs to the mouse transcriptome demonstrated that 9124 mouse transcripts, representing 6701 genes, are covered by more than 95% of their sequence length. Metabolic pathways of the central carbohydrate metabolism and biosynthesis routes of sugars used for protein N-glycosylation were reconstructed from the transcriptome data. All relevant genes representing major steps in the N-glycosylation pathway of CHO cells were detected. The present manuscript represents a data set of assembled and annotated genes for CHO cells that can now be used for a detailed analysis of the molecular functioning of CHO cell lines. (C) 2011 Elsevier B.V. All rights reserved.