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Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing

Paper ID Volume ID Publish Year Pages File Format Full-Text
23741 43468 2011 9 PDF Available
Title
Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing
Abstract

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.

► We sequenced the CHO cell line transcriptome with pyrosequencing technology from 454 Life Sciences generating sequence reads of ≈400 bp. ► These long reads enabled a de novo assembly of the generated transcriptome data with regard to the exon-intron structure of eukaryotic transcripts. ► We assembled more than 29,000 transcripts and are able to distinguish between different isoforms of genes. ► Finally, we publish assembled data to enable further research to other scientific groups.

Keywords
CHO cells, Chinese hamster ovary cells; EST, expressed sequence tag; NGS, next-generation sequencingChinese hamster ovary cell; cDNA; Next-generation sequencing; N-Glycosylation pathway
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Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 156, Issue 3, 10 December 2011, Pages 227–235
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us