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 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.
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
Chinese hamster genome database. http://www.chogenome.org (date of download or visit).
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.