News
Updated chromosome-scale CH assembly and CH/CHO-K1 annotations
January 27, 2021
A significantly more continuous version of the Chinese hamster genome, CH PICRH (GCF_003668045.3), along with its 2020 RefSeq annotation is now on CHOgenome.org. Long-range scaffolding of the previous CH genome assembly was performed using high-throughput chromosome conformation capture (Hi-C) and now 97% of the genome is contained in 11 large scaffolds corresponding to the CH chromosomes. In addition, the updated 2020 RefSeq annotation for the CHO-K1 cell line is available. Both can be searched (gene search and BLAST) and viewed on JBrowse. More information on the most recent version of the Chinese hamster genome can be found here.
Updated CH assembly and CH/CHO-K1 annotations
May 1, 2019
We are excited to announce that the significantly improved Chinese hamster genome, CH PICR (GCF_00366804.1), along with its 2018 RefSeq annotation is now online. In addition, an updated RefSeq annotation for the CHO-K1 cell line is now available. Both can be searched (gene search and BLAST) and viewed on JBrowse. More information on the updated Chinese hamster genome can be found here.
New mRNA Expression Browser (Beta)
June 7, 2017
The browser (beta version) for the visualization of mRNA expression from CHO-K1 cells is now online. The data is from several published DNA-microarray or RNA-Seq experiments. The tutorial on how to use this browser 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.