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 forseeable 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 community plans to collect third generation sequencing data (PacBio) on the hamster to help create a new reference assembly. If you are interested in learning more or making a donation, please vist the CHOStart webpage for more details.
|The Chinese Hamster (8May2014) and CHO-K1 RefSeq (8May2014) annotations are now available.
|Search CHO-K1 (8May2014) assembly by gene name or symbol:
|Search Chinese hamster RefSeq (8May2014) assembly by gene name or symbol:
|Additional updates to the CHOgenome search are coming.
Your query may take up to one minute, depending on the number of hits in the RefSeq assembly database.
Please read the database disclaimer.
- Update [July 1, 2014]
- CHOgenome.org will be unavailable on Thursday, July 3rd from 6 am to 6 pm EST. Please plan accordingly and we apologize for any inconvenience.
- Update [June 27, 2014]
- The BLAST server will periodically be unavailable for the next few days to permit updates to be made.
- Update [May 27, 2014]
- 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.
- Update [May 12th, 2014]
- CHOStart: A crowdfunding request for PacBio hamster sequencing.
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. Click here to learn more about CHOstart and how to donate
- Contact: CHOgenome@dbi.udel.edu
- Goal: $60,000
Current Commitments: $20,000
- Update [December 19, 2013]
- Update [December 10, 2013]
- A protein BLAST database for the Brinkrolf et al. chromosomal Chinese Hamster genome released in August has been added to the CHO Genome Databases.
- Update [November 21, 2013]
- 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.
- Update [October 11, 2013]
- Nucleotide BLAST databases for both Chinese Hamster genomes released in 2013 have been added to the CHO Genome Databases.
- Update [August 15, 2013]
- 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.
- Update [July 29, 2013]
- 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.
- Update [June 3, 2013]
- 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.
- Update [November 1, 2012]
- 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.
- Update [October 16, 2012]
- The international community's effort was recognized as a finalist at the 2012 Bioprocess International Awards ceremony in Providence, RI. Our efforts were nominated as part of the Upstream Collaboration of the Decade. According to the BPI website:
"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.
- Update [August 14, 2012]
- 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.
- Update [June 5, 2012]
- 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.
- Update [April 17, 2012]
- A BETA version of the CHO GBrowse genome viewer is now available and can be accessed using the Genome Viewer icon above or by clicking here. The genome browser currently hosts the CHO-K1 RefSeq genome assembly (Assembly ID GCF_000223135.1).
- Update [April 13, 2012]
- 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.
- Update [January 6, 2012]
- CHO gene coexpression database (CGCDB), a new online database of gene coexpression patterns derived from industrial cell culture of CHO cells, can be accessed at www.cgcdb.org.
Chinese Hamster Database ver 1.0