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2012 LEGACY SITE:
Chinese Hamster
Genome Database
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CHO Genomic Data Resources
This is a temporary page containing links to relevant publications and public data sets. Links to next generation sequencing raw data in the Sequence Read Archive (SRA) are provided when available. Journal access may be limited to subscribed users.
Genome
| Description |
Title |
Reference |
| A chromosome sorting approach was used to facilitate genome assembly from short-read sequences of the Chinese hamster genome |
Chinese hamster genome sequenced from sorted chromosomes |
Brinkrolf K et al. Nature Biotechnol (2013) 31, 694-695 |
| Draft genomic sequence of the Chinese hamster and resequencing of CHO-K1, DG44, and CHO-K cell lines |
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome |
Lewis N et al. Nature Biotechnol (2013) 31, 759-765 |
| Generation of a physical chromosome map of the CHO-DG44 cell line. |
Construction of BAC-based physical map and analysis of chromosome rearrangement in Chinese hamster ovary cell lines. |
Cao Y et al. Biotechnol Bioeng (2012) 109, 1357-1367 |
| CHO BAC library sequences |
| Draft genomic sequence and analysis of the ancestral CHO-K1 cell line. |
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. |
Xu X et al. Nature Biotechnol (2011) 29, 735–741 |
| GenBank AFTD00000000.1 |
| WGS record AFTD01 |
| CHO-K1 genome SRA040022 |
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CHO-K1 transcriptome SRA040045 |
| Low coverage genome sequencing of a recombinant CHO cell line. |
Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology. |
Hammond S et al. BMC Genomics (2011) 12, 67 |
| SRA012218 |
Proteome
Transcriptome
| Description |
Title |
Reference + Links |
| Coexpression analysis of transcriptional profiling of CHO cell lines using microarray data identifies clusters of coexpressed genes associated with bioprocess phenotypes. |
Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity. |
Clarke C et al. J Biotechnol (2011) 155, 350-359 |
| Transcriptome profiling of CHO-K1 and CHO-DUKXB11 cells grown under varying culture conditions. |
Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. |
Becker J et al. J Biotechnol (2011) 156, 227-235 |
| CHO transcriptome shotgun assembly (TSA) |
| Expression profiling of a recombinant CHO line cell under varying conditions. |
Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing. |
Birzele F et al. Nucleic Acids Res (2010) 38, 3999-4010 |
| SRA010967 |
Non-coding RNA
| Description |
Title |
Reference + Links |
| CHO cell small RNA sequencing data is used to predict piRNAs |
Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data |
Gerstl M et al. J Biotechnol (2013) 166, 51-57 |
| Conserved miRNAs identified from CHO-K1 and two recombinant CHO cell lines. miRNA data included in supplemental material. |
Profiling conserved MicroRNA expression in recombinant CHO cell lines using Illumina sequencing. |
Hammond S et al. Biotechnol Bioeng (2012) 109, 1371-1375 |
| SRA048985 |
| Identification of 212 CHO miRNA sequences. Precursor miRNA sequences included in supplemental material. |
Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. |
Hackl M et al. J Biotechnol (2012) 158, 151-155 |
| miRNAs identified from parental and recombinant CHO-K1 and CHO-DUXB11 cells under varying conditions. miRNA data included in supplemental material. |
Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. |
Hackl M et al. J Biotechnol (2011) 153, 62-75 |
| SRA024456 |
| miRNAs identified from parental and recombinant CHO-K1 and CHO-DG44 cells under varying conditions. miRNA data included in supplemental material. |
Conserved microRNAs in chinese hamster ovary cell lines. |
Johnson KC et al. Biotechnol Bioeng (2011) 108, 475-80 |
Nucleotide and Protein Sequences
CHO Community Requests
CHO Community Links
| Description |
Title |
Reference + Links |
| CGCDB provides access to gene coexpression patterns derived from microarray analysis of transcript expression in CHO cells. |
CGCDB: A Web-Based Resource for the Investigation of Gene Coexpression in CHO Cell Culture. |
CHO gene coexpression database at www.cgcdb.org |
| Clarke C et al. Biotechnol Bioeng (2012) 109, 1368-1370 |
| GO terms from CHOgenome and gene ontology for CHO gene symbols |
Complete List of CHO gene GO terms |
CHO GO terms |