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.
ESACT meeting
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.