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.
Tutorial 2 – Overview of CHOgenome.org
August 2014, Version 2.0
Click here for PDF version.
The website for the Chinese hamster genome database is http://www.CHOgenome.org.
The homepage provides access to the underlying database, as well as to the Chinese hamster-specific genomic tools and community resources.
The Version 2.0 tutorials outline the CHOgenome.org website as of August 2014. The legacy website (Version 1.0) will remain available at www.CHOgenome.org/legacy.html, but will not be updated after August 2014.
Users can return to the homepage at any time by clicking on the Home heading on the far left of the navigational menu.
A News section on the left side of the homepage displays the most recent news items, while an Events section on the right side of the homepage displays the upcoming and most recent events. Additional events and news items can be viewed by selecting the see all link at the bottom of the respective section or by selecting the News or Events links from the General Info tab of the menu bar.
Questions or comments can be sent to the CHO genome website management team by clicking on thebutton located at the bottom of all the CHO genome webpages. Please communicate any issues you encounter or pertinent feedback and a CHO genome representative will provide a timely response.
The Info section in the center contains a comprehensive gene search box for all the NCBI RefSeq Chinese hamster genome databases, a welcome statement, and icons that serve as direct links to the genomic tools. The icons include: (1) a Gene Search icon that leads to the advanced RefSeq search page, (2) a BLAST icon that provides access to the 13 Chinese hamster databases hosted on the CHO BLAST server, (3) a Genome Viewer icon that leads to the GBrowse tool to allow users to see whole scaffolds with full annotations, (4) a Proteome Browser icon that provides access to the CHO proteome databases consisting of the 2D-PAGE and Shotgun results, and (5) a Downloads icon that leads to the Chinese hamster-specific data section.
The blue navigational menu located at the top of each page on the CHO genome website enables quick access to the Chinese hamster-specific tools and resources. Several of the main sections (General Info, Genomes, and Resources) are drop down menus with multiple options that can be accessed by moving the cursor over the main section title.
General Information Tab
The General Info section contains direct links to the About, News, Tutorials, and Events pages.
- The About page contains a brief history of the CHO genome community, a brief introduction to the goals of this resource, the current and future plans, instructions for citing this resource, and the disclaimer.
- The News page contains news updates since 2012.
- The Events page contains the complete list of upcoming conferences of interest to the CHO community and highlights of past workshops and conferences.
- The Tutorials page contains six tutorials that can be downloaded and used to assist users with navigating and using CHOgenome.org. The six tutorials include: (1) an overview of the CHO genome resource, (2) an overview of CHOgenome.org, (3) assistance with searching the Chinese hamster genome databases, (4) BLAST searching the Chinese hamster genome, (5) viewing the Chinese hamster genomes, and (6) searching the Chinese hamster proteome databases.
Search pages for the RefSeq Chinese hamster (CH) and CHO cell line, GenBank CHO-K1, and CH mitochondrial genomes are each accessible from this tab.
For additional details, please see Tutorial #3, Searching the Chinese Hamster Genome Database.
- The comprehensive CH & CHO RefSeq search page enables users to select the RefSeq Chinese hamster genome(s) to be searched and the search terms to search against.
- The CHO-K1 GenBank (2011) genome can be searched by accession number, gene name or symbol, or GO term.
- The CH Mitochondria can only be searched by gene symbol.
The tools and resources relevant to the CHO Community are accessible from this menu.
- The BLAST section contains 13 nucleotide and amino acid CH databases for BLAST searches.
- For additional details, please see Tutorial #4, BLAST Searching the CHO Genome.
- The GBrowse section contains a genome viewer tool for the CHO-K1 RefSeq (2012) assembly, which enables users to visualize searched genes and scaffolds.
- For additional details, please see Tutorial #5, Viewing the CHO & CH Genomes.
- The Proteome Browser section contains 2D PAGE and Shotgun databases of proteins previously identified by the Chinese hamster community.
- For additional details, please see Tutorial #6, Searching the Proteome Database.
- The Data section provides links to relevant publications and public data sets.
The Partners section provides a visual list of the agencies, corporations, and universities actively supporting this CHO genome initiative. Each logo serves as a direct link to the website associated with the respective partner.
- To become a partner, select the Contact Us button and a CHO genome representative will respond.