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.
CHO Genome Workshop
November 15 - November 18, 2010
Visit www.genomeconference.org for more information.
November 17, 2010 was the day that the Chinese hamster ovary cell community entered the genome era!
CHO Genome Workshop Summary
The workshop opened with remarks from Kelvin Lee who gave a history of how the community came together and Bernhard Palsson who provided context on the use of CHO cells in the biotechnology industry.
The talks included:
- Xu Xun gave the first ever detailed description of the CHO K1 genome and described many features of the CHO genome.
- Takeshi Omasa provided an overview of physical mapping and karyotyping efforts on CHO, highlighting the dynamic nature of the chromosomes.
- Steve Quake discussed efforts to characterize the CHO exome using a variety of techniques and assembly of these data in the context of mouse data.
- Nicole Borth presented an analysis of CHO microRNA including some possibly new microRNAs that have not been reported previously.
- Gyun-Min Lee gave a detailed overview of the use of proteomic methods to characterize CHO cells and particular CHO phenotypes of interest.
- Lars Nielsen provided an important description of how genome-scale flux analysis models can be developed - something that is now possible with a CHO genome.
- Bernhard Palsson then discussed specific aspects of the CHO K1 genome included a coarse-grained analysis (relative to mouse, rat, human), a functional analysis (glycosyltransferases and viral susceptibility genes), and individual genes (p53 and EGFR).
Finally, Mike Betenbaugh and Kelvin Lee led a discussion of next steps for our community. These include the importance of sequencing the hamster and other cell lines as well as having a simple framework for the community to interact with these data.