News

Coming Soon!

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.

CHOmine (BETA-Version)

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.

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Genomic Data Resources

This web page contains 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.

Click here to access the original CH and CHO genome data files that are hosted in our own Cricetulus griseus File Archive.

Genome

Description Title Reference
CHO cell genome-scale metabolism model with 1,766 genes, 6,663 reactions, and integrated -omics data findings A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism Hefzi H et al. Cell Systems (2016) 3, 434-443.
Zipped CHO, CHO-K1, CHO-S, and CHO-DG44 cell line-specific models [.ZIP file]
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
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

Description Title Reference + Links
Analysis of CHO-K1 proteome and secretome. Proteomic Analysis of Chinese Hamster Ovary Cells Baycin-Hizal D et al. J Proteome Res (2012)
Supplementary Table 1

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

Epigenome

Description Title Download Link
Investigation of genome and epigenome changes in response to evolutionary pressures. All the corresponding data, including genome sequences for 6 cell lines, SNPs, indels, translocations etc, full genome methylation data, and data on histone modifications during a batch culture are hosted on an online database. Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time Epigenome Database
Feichtinger et al. Biotechnol Bioeng (2016) DOI: 10.1002/bit.25990

Nucleotide and Protein Sequences

Description Title Download Link
GenBank Assembly (ID GCF_000223135.1)
A FASTA file of all nucleotide sequences in the CHO-K1 GenBank database. CHO_EMBL.fasta Download CHO_EMBL.fasta
A FASTA file of all protein sequences in the CHO-K1 GenBank database. CHO_EMBL_protein.fasta Download CHO_EMBL_protein.fasta
RefSeq Assembly (ID GCF_000223135.1)
A FASTA file of all nucleotide sequences in the CHO-K1 RefSeq database. CHO_refseq_transcript.fasta Download CHO_refseq_transcript.fasta
A FASTA file of all protein sequences in the CHO-K1 RefSeq database. CHO_refseq_protein.fasta Download CHO_refseq_protein.fasta

CHO Community Files & Links

Description Title Download Link
An excel file containing the RefSeq (2014) CHO-K1 and CH genes with prime notation in the gene name/gene description. CompleteList2014PrimeGenes.xlsx Download CompleteList2014PrimeGenes.xlsx
A text file of GenBank assembly CHO genes and the associated mouse, rat, and human homologs CHOhomologs_012312.txt Download CHOhomologs_23Jan12.txt
A text file of CHO gene accession numbers, symbols, and the associated GO functions. CHO_GO_Functions_12Sep13.txt Download CHO_GO_Functions_12Sep13.txt
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
An excel file of all the RefSeq (2014) CH and CHO-K1 transcript homologs. CH_CHO_transcript_homolog_2014.xlsx Download CH_CHO_transcript_homolog_2014.xlsx