Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines

Abstract

Chinese hamster ovary (CHO) cell lines represent the most commonly used mammalian expression system for the production of therapeutic proteins. In this context, detailed knowledge of the CHO cell transcriptome might help to improve biotechnological processes conducted by specific cell lines. Nevertheless, very few assembled cDNA sequences of CHO cells were publicly released until recently, which puts a severe limitation on biotechnological research. Two extended annotation systems and web-based tools, one for browsing eukaryotic genomes (GenDBE) and one for viewing eukaryotic transcriptomes (SAMS), were established as the first step towards a publicly usable CHO cell genome/transcriptome analysis platform. This is complemented by the development of a new strategy to assemble the ca. 100 million reads, sequenced from a broad range of diverse transcripts, to a high quality CHO cell transcript set. The cDNA libraries were constructed from different CHO cell lines grown under various culture conditions and sequenced using Roche/454 and Illumina sequencing technologies in addition to sequencing reads from a previous study. Two pipelines to extend and improve the CHO cell line transcripts were established. First, de novo assemblies were carried out with the Trinity and Oases assemblers, using varying k-mer sizes. The resulting contigs were screened for potential CDS using ESTScan. Redundant contigs were filtered out using cd-hit-est. The remaining CDS contigs were re-assembled with CAP3. Second, a reference-based assembly with the TopHat/Cufflinks pipeline was performed, using the recently published draft genome sequence of CHO-K1 as reference. Additionally, the de novo contigs were mapped to the reference genome using GMAP and merged with the Cufflinks assembly using the cuffmerge software. With this approach 28,874 transcripts located on 16,492 gene loci could be assembled. Combining the results of both approaches, 65,561 transcripts were identified for CHO cell lines, which could be clustered by sequence identity into 17,598 gene clusters.

The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells

“…by molecular engineering approaches, is of great interest to academia and industry (Baik and Lee, 2014). An essential basis for this purpose is the CHO K1 genomic sequence and transcriptome data that became recently available and will enable a deeper understanding of genotype-phenotype relationships in terms of product quality attributes (Baik and Lee, 2014;Lewis et al, 2013;Rupp et al, 2014). A missing link between these cellular levels in CHO cells, however, is the yet unknown CHO cell epigenome.…”

Binning enables efficient host genome reconstruction in cnidarian holobionts

“…[59]. The functional annotation of predicted genes was conducted within the GenDBE annotation platform for eukaryotes [60]. To assess the quality of gene prediction, RNA-seq data were mapped onto the genome sequences.…”

The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms

“…The different gene predictions were combined with the Evidence Modeler EVM (Haas et al, 2008) using the protein mapping as supporting information. The C. jadinii genome sequence and the gene prediction were uploaded into the open source genome annotation system GenDBE (Rupp et al, 2014). The integrated automatic functional annotation was computed using Metanor-Euk (Rupp et al, 2014).…”

“…The C. jadinii genome sequence and the gene prediction were uploaded into the open source genome annotation system GenDBE (Rupp et al, 2014). The integrated automatic functional annotation was computed using Metanor-Euk (Rupp et al, 2014). 2.7.…”