March 10, 2017
Users will be able to visualize CHO cell mRNA expression data either from published DNA-microarray or RNA-Seq experiments via JBrowse. The visualized data will enable users to easily obtain gene expression levels and compare gene expression levels among different conditions.
August 19, 2016
CHOmine, the InterMine site for CHO and Chinese hamster, went online on August 11, 2016 at https://chomine.boku.ac.at/. CHOmine collects and integrates publicly available Chinese hamster and CHO data, where different datasets are connected to provide user-friendly access. Currently, users are asked to test the site and to provide feedback (impressions, comments, issues, and suggestions for improvements) to Matthias.Gerstl@acib.at or Nicole.Borth@boku.ac.at.
CHO Epigenomic Data
April 14, 2016
A new database of epigenomic information (cho-epigenome.boku.ac.at) for 6 CHO cell lines has been created by Dr. Nicole Borth's group. A link to this database has been added to CHOgenome.org's Data webpage. The epigenomic database website hosts genome sequences for 6 cell lines, SNPs, structural variants, full genome methylation data, and batch culture histone modification data. The manuscript describing the acquisition and analysis of the data can be found here.
May 15 - May 18, 2011
Visit www.esact2011.com for more information.
CHO Genome Workshop Summary
The CHO genome workshop, with more than 220 participants, opened with three talks describing the generation of draft genome sequences for several CHO cell lines and the Chinese hamster followed by three talks demonstrating how this information can be leveraged in metabolic and transcriptomic studies to aid in cell line engineering.
The talks included:
- Bernhard Palsson described the draft genome of CHO-K1 and a comparative genomic analysis of six additional CHO cell lines.
- Bernard Loo presented a draft genome assembly and annotation of the Chinese hamster and outlined efforts to identify transcriptional start sites and regulatory elements.
- Nicole Borth described a draft genome assembly of the Chinese hamster by integrating multiple NGS technologies and efforts to identify and annotate splice variants.
- Iman Famili described the application of a metabolic model for CHO cells in media optimization and development of novel vector systems.
- Colin Clarke presented a model to predict CHO cell productivity based on gene expression profiles of temperature-shifted CHO cell lines.
- Jeoffrey Schageman described a comparative transcriptomic analysis of CHO cells lines under varying culture conditions that can identify gene co-expression patterns.
After the workshop, Mike Betenbaugh and Kelvin Lee led a discussion of the development of and the next steps for the CHO community-based website, www.CHOgenome.org.