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 6 – Searching the Proteome Database
August 2014, Version 2.0
Click here for PDF version.
The Chinese hamster proteome database can be reached by selecting the "Proteome" resource from the menu bar or by selecting the "Proteome Browser" button from the homepage.
The address for the Chinese hamster proteome database is http://www.CHOgenome.org/proteome.php.
The proteome database provides access to the proteomic data generated from CHO cell lines. This database hosts protein data from 2D polyacrylamide gel electrophoresis (2D PAGE) gels and shotgun proteomics analysis.
To have your data included, please contact us at firstname.lastname@example.org.
2D PAGE Database
The 2D PAGE database is accessed by selecting the 2D PAGE Results button.
The webpage has the complete list of 2D gels available for public search with a small image of the gel and the publication information, if it has been published.
Selecting an image leads to a much larger image of the gel with a link to the reference (if applicable).
Selecting a quadrant (if the total number of identified proteins is large) leads to a table of the identified proteins, a labeled 2D gel, and links to the NCBI protein and the CHO Genome gene pages.
Shotgun Proteomics Database
The shotgun proteomics database is accessed by selecting the Shotgun Results button.
The shotgun proteomics database consists of the protein sets submitted to the CHO genome website. The publication for each dataset (if applicable) is listed following the description of each dataset. The link connects to the Publications page on the CHO genome website, which contains the links for the relevant publications.
The shotgun proteome database is searchable by protein name. The results page consists of all matches from the selected datasets. The protein name and accession identification are provided for each result.
Selection of the accession identification yields the specific details from the identification. These details can consist of the protein name, accession ID, the peptide sequences that were identified, the number of identified sequences, coverage, FDR, and other experiment specific details of possible relevance, including the cluster ID, group ID, SwissProt Annotation Homology, GO annotation, and Sequence ID.