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.
About
CHO Genome Community
The Chinese hamster (Cricetulus griseus) ovary (CHO) cell line was first isolated by Puck (J. Exp. Med. 1958; 108: 259-271) more than 50 years ago. Currently, CHO cells are the most important cell line for production of biopharmaceuticals. The 2012 CHO-produced biopharmaceutical sales totaled nearly US$ 65 billion, more than half the 2012 biopharmaceutical sales total of US$ 125 billion (La Merie Publishing. "R&D Pipeline News." PipelineReview.com. 7 May 2013.). CHO cells offer tremendous promise for production of vaccines as well as in their ongoing critical role as a transfection host for understanding gene function. Despite the scientific and economic importance of this cell line, there is no publicly available genome sequence information for CHO cells.
A Resource for CHO Cell Genomics
Based on an open source model, the mission of the CHOgenome.org User Group is to share genome-scale information on Chinese Hamster Ovary cells to the international scientific community.
This website, currently hosted at the University of Delaware, is dedicated to hosting data and resources to support the international community working with CHO cells.
We are building the infrastructure to support genome sequencing activities through an international not-for-profit community-based effort.
| For more information, feel free to contact: | Kelvin Lee (Univ. Delaware; KHL at udel dot edu) Nicole Borth (BOKU; nicole dot borth at boku dot ac dot at) Michael Betenbaugh (Johns Hopkins Univ.; beten at jhu dot edu) |
What is planned for CHOgenome.org?
 |
| photo courtesy of Nicole Borth |
Currently we are developing the framework for:
- Hosting the latest CHO genome updates
- Providing genome browsing and annotation tools
- Linking to other genomic databases
- Hosting proteomic data
Future plans include:
- Hosting transcriptomic and metabolomic data
- Developing a user forum and other community features
- Providing support for the development of user tools, such as siRNA or microRNA screens
How to Cite this Resource
Kremkow BG, Baik JY, MacDonald ML, and Lee KH. "CHOgenome.org 2.0: Genome resources and website updates." Biotechnol J (2015) 10, 931-938.
OR
Hammond S, Kaplarevic M, Borth N, Betenbaugh MJ, and Lee KH. "Chinese Hamster Genome Database: An Online Resource for the CHO Community at www.CHOgenome.org."Biotechnol Bioeng (2012) 109, 1353-1356
OR
Chinese hamster genome database. http://www.chogenome.org (date of download or visit).
Disclaimer
The data and information released by CHOgenome.org are provided "as is" and may contain errors and be incomplete. Data and information are provided without warranty of any kind, including without limitation, warranties of merchantability, fitness for a particular purpose, and non-infringement. Any reproduction or use for commercial purpose is prohibited without the prior written permission of the CHOgenome.org User Group.