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.
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.
A featured article section has been added to the homepage, where articles of potential interest to the CHO community will be posted periodically. The current and past featured articles will be archived in the new "Featured Articles" page which can be accessed through the Resources tab.
The 2012 tracks have been added to the CHO-K1 JBrowse genome viewer tool. In addition, the 2014 Chinese hamster RefSeq browser has been created with annotation tracks. A new portal page provides access to these browsers by selecting the Genome Viewer tab or button. Also, new links are available in the RefSeq gene details page that link directly to the appropriate JBrowse viewer and scaffold.
The BLAST and File Archive tools have been successfully updated. If you experience any issues, please let us know.
The CHOStart project has generated 170 SMRT cells and 95 GB of genomic sequence data so far. Thanks to your support, we have raised ~40% of the fundraising goal.
The CHOStart project has generated 84 SMRT cells and 42 GB of genomic sequence data so far. Thanks to your support, we have raised ~30% of the fundraising goal. More details and updates regarding the CHOStart project can be found here.
The genome viewer tutorial has been updated with the instructions on how to use JBrowse. The tutorials can be found under the "General Info" tab. Another JBrowse instance has been added as well, which contains the nucleotide sequence of the Chinese Hamster chromosomes (from Brinkrolf K et al).
The CHO-K1 genome viewer has been updated from GBrowse to JBrowse, and contains the most up to date annotations (from 2014). The GBrowse instance for the 2012 annotated version of CHO-K1 is still available in the legacy version of the website (linked at the bottom of this page). The updated tutorial for viewing the genomes in JBrowse will be posted shortly.
We're getting a facelift in the near future!
The updates will provide a more organized approach to searching the data and going through results - especially important given the recent release of new genomes. Don't worry: all of the legacy genomes (CHO-K1 GenBank, and earlier CHO-K1 RefSeq) will be maintained on the website and will still be searchable. In fact, we will keep legacy pages operational for the foreseeable future in case you like the current look and feel.
As always, please let us know of any unusual or unexpected issues and to share your feedback on the new look and feel.
The BLAST server will periodically be unavailable for the next few days to permit updates to be made.
The community plans to collect third generation sequencing data (PacBio) on the hamster to help create a new reference assembly. We expect the effort to cost $60,000. We request support from the community. The suggested support level is $5000 per organization, although amounts larger and smaller are welcome. Contributions from U.S. organizations are tax deductible. Our timeline is to collect all data by end of 2014 and to manually correct automated annotations through 2015. Any funds collected over our $60,000 target will support the annotation effort.
The C_griseus_v1.0 and CriGri_1.0 annotations (assemblies GCF_000419365.1 and GCF_000223135.1, respectively) have been released. We expect to have this data available soon.
A protein BLAST database for the Brinkrolf et al. chromosomal Chinese Hamster genome released in August has been added to the CHO Genome Databases.
Everyone is welcome to join the community at the upcoming workshop in Vienna in March!
The Chinese hamster genome assembly will be added to the CHO genome databases upon the final release of both the Chinese hamster genome annotations (Lewis et al. and Brinkrolf et al.). Until that point, the Chinese hamster genome scaffold nucleotide sequences have been added to the BLAST databases.
Nucleotide BLAST databases for both Chinese Hamster genomes released in 2013 have been added to the CHO Genome Databases.
Nature Biotechnology published another sequencing paper relevant to the CHO community. The Chinese hamster genome was sequenced from sorted, individual chromosomes. This genome provides a quality reference to permit the study of CHO cell line chromosomal rearrangements and stability.
Nature Biotechnology published another CHO sequencing paper. The draft genome sequence of the female Chinese hamster, Cricetulus griseus, was reported in addition to the resequencing of 6 CHO cell lines, including CHO-K1, DG44, and CHO-S. Further updates will be posted when the genomic information has been released and added to the CHO Genome Databases.
A CHOgenome.org workshop will take place at the ESACT Meeting on Sunday, June 23 at 13:45. The title of the workshop is "The www.CHOgenome.org Resource for the International CHO Biotechnology Community?" The workshop will include presentations on current applications of genome scale information, where it is useful, and how has it helped in different research efforts, followed by discussion on the next steps for the cell culture community surrounding the CHO Genome effort.
Data for 6163 proteins from analysis of the CHO proteome and secretome is now available at the CHO Genomic Resources Data page, under the section titled Proteome. Detailed data is expected to be available in the next few weeks.
"The Collaboration of the Decade Award recognizes industry alliances and collaborations whose innovative partnerships dramatically transformed stand-alone technologies. These collaborations result in overall process cost reduction while creating new, effective approaches to biopharmaceutical design, development, and manufacturing."
We are grateful for the support and engagement of the broad international community in sequencing of CHO and related genomes to improve bioprocessing.
CHO proteomic information and RNA sequences are currently being analyzed and incorporated into the database. These updates are expected to be available within the next few weeks.
A BETA version of the CHO RefSeq genome database is now available. This database hosts the CHO-K1 RefSeq genome assembly (Assembly ID GFC_000223135.1) released by NCBI in November 2011.
There are two genome assemblies available for the CHO-K1 genome: the CriGri_Aug2011 GenBank genome assembly released in August 2011 and the CHO-K1 RefSeq genome assembly, released by NCBI in November 2011.
The CHO-K1 genome database ver1.0 currently hosts the CriGri_Aug2011 GenBank genome assembly and we are working to add the CHO-K1 RefSeq genome assembly.