The authors evaluated the RNA-seq mapping of four CHO cell reference sequences hosted by the NCBI RefSeq. The reference sequences were the 2012 annotated CHO-K1 genome, the 2014 annotated Chinese hamster genome, and their respective transcriptomes. The 2014 Chinese hamster genome had the best total mapping rate of RNA-seq data (73.5%) and the total mapping rate could be improved by approximately 15% with the addition of the human and mouse genomes.
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.
Gene Names with Prime Notation
June 24, 2015
Within the 2014 RefSeq annotations, 211 genes were recently identified as having not been loaded in the CHOgenome.org databases due to coding algorithm errors caused by prime notation (e.g. - 3' or 5') in the gene's name and product description. These errors have been rectified and the 211 genes, 115 genes in the 2014 CHO-K1 annotation and 96 genes in the 2014 CH annotation, have been correctly loaded to their respective CHOgenome.org databases. The complete list of these genes can be found on the Data tab in the CHO Community Files & Links section.
Search the RefSeq Chinese Hamster and CHO-K1 assemblies
BLAST sequences against Chinese Hamster or CHO-K1 genomes
View the annotated RefSeq Chinese Hamster or CHO-K1 genomes
Search the 2-D gel and shotgun datasets
Useful Chinese Hamster publications and files
CH Genome Viewer
View the chromosome-sorted Chinese Hamster genome
Mammalian Systems Biotechnology Workshop
August 11 - August 12, 2016
This workshop will bring together globally eminent experts actively working in the Mammalian Systems Biotechnology field, in order to share and discuss state-of-the-art developments and their industrial applications.
The 251st ACS National Meeting & Exposition in San Diego, CA will convene from March 13 - 17, 2016 and the BIOT division will focus on the exchange of information among academic and industrial researchers regarding technology utilizing life-based systems to produce useful products and services.