CHOgenome.org
Genomic Data Resources
News
Updated chromosome-scale CH assembly and CH/CHO-K1 annotations
January 27, 2021
A significantly more continuous version of the Chinese hamster genome, CH PICRH (GCF_003668045.3), along with its 2020 RefSeq annotation is now on CHOgenome.org. Long-range scaffolding of the previous CH genome assembly was performed using high-throughput chromosome conformation capture (Hi-C) and now 97% of the genome is contained in 11 large scaffolds corresponding to the CH chromosomes. In addition, the updated 2020 RefSeq annotation for the CHO-K1 cell line is available. Both can be searched (gene search and BLAST) and viewed on JBrowse. More information on the most recent version of the Chinese hamster genome can be found here.
Updated CH assembly and CH/CHO-K1 annotations
May 1, 2019
We are excited to announce that the significantly improved Chinese hamster genome, CH PICR (GCF_00366804.1), along with its 2018 RefSeq annotation is now online. In addition, an updated RefSeq annotation for the CHO-K1 cell line is now available. Both can be searched (gene search and BLAST) and viewed on JBrowse. More information on the updated Chinese hamster genome can be found here.
New mRNA Expression Browser (Beta)
June 7, 2017
The browser (beta version) for the visualization of mRNA expression from CHO-K1 cells is now online. The data is from several published DNA-microarray or RNA-Seq experiments. The tutorial on how to use this browser can be found here.
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 |
|---|---|---|
| Further improved genome assembly (PICRH) for the Chinese hamster with chromosome-scale scaffolds. Long‐range scaffolding of PICR was performed using high‐throughput chromosome conformation capture. | Chromosome‐scale scaffolds for the Chinese hamster reference genome assembly to facilitate the study of the CHO epigenome | Hilliard et al. Biotechnol Bioeng (2020) 117, 2331-2339 |
| An improved genome assembly (PICR) for the Chinese hamster that was created using short-read sequencing from previous CH assemblies and new long-read sequencing data. | A reference genome of the Chinese hamster based on a hybrid assembly strategy | Rupp et al. Biotechnol Bioeng (2018) 115, 2087–2100 |
| 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 |
Gene Ontology (GO) Terms
| Description | Title | Download Link |
|---|---|---|
| A CSV file of CH PICRH gene accession numbers and associated GO terms. | CH_PICRH_GO_terms_Apr2021.csv | Download CH_PICRH_GO_terms_Apr2021.csv |
| A CSV file of CHO-K1 gene accession numbers and associated GO terms. | CHO-K1_GO_terms_Apr2021.csv | Download CHO-K1_GO_terms_Apr2021.csv |
| A CSV file of CH PICR gene accession numbers and associated GO terms. | CH_PICR_GO_terms_Apr2021.csv | Download CH_PICR_GO_terms_Apr2021.csv |
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 |
| 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 |