ArticleNucleic acids research2010
Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
36 citing papers in PubMed, 97 citations in OpenAlex.
- Improving recombinant protein productivity in CHO cells via multi-omics data integration.Bioresources and bioprocessing · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Resolvin D1 in the Lipopolysaccharide-Induced Inflammatory Microenvironment Mediates Resolution in Human Monocytic THP-1 Cells.Biomedicines · 2026Article
- Transcriptomic Insights Into Serum-Free Medium Adaptation and Temperature Reduction in Chinese Hamster Ovary Cell Cultures.Biotechnology journal · 2025Article
- Allelopathic Molecular Mechanisms of the Two Main Allelochemicals in Sweet Potato.Current issues in molecular biology · 2024Article
- Evaluation of PepT1 (SLC15A1) Substrate Characteristics of Therapeutic Cyclic Peptides.Pharmaceutics · 2022Article
- Transcriptome Analysis of the Japanese Pine Sawyer Beetle,Journal of fungi (Basel, Switzerland) · 2021Article
- Evolution from adherent to suspension: systems biology of HEK293 cell line development.Scientific reports · 2020Article
- Comprehensive Glycoproteomic Analysis of Chinese Hamster Ovary Cells.Analytical chemistry · 2018Article
- Bioinformatic analysis of Chinese hamster ovary host cell protein lipases.AIChE journal. American Institute of Chemical Engineers · 2018Article
- Molecular mechanisms of tannin accumulation in Rhus galls and genes involved in plant-insect interactions.Scientific reports · 2018Article
- Differently expressed long noncoding RNAs and mRNAs in TK6 cells exposed to low dose hydroquinone.Oncotarget · 2017Article
- An RNA-seq transcriptome analysis of floral buds of an interspecific Brassica hybrid between B. carinata and B. napus.Plant reproduction · 2014Article
- [Differential expression profiles of microRNAs/mRNA and docking study in oral squamous cell carcinoma].Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology · 2014Article
- A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat.Molecular pain · 2014Article
- Article
- Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.PloS one · 2014Article
- Article
- A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird.PloS one · 2014Article
- CHO microRNA engineering is growing up: recent successes and future challenges.Biotechnology advances · 2013Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The arrival of next-generation sequencing (NGS) technologies has led to novel opportunities for expression profiling and genome analysis by utilizing vast amounts of short read sequence data. Here, we demonstrate that expression profiling in organisms lacking any genome or transcriptome sequence information is feasible by combining Illumina's mRNA-seq technology with a novel bioinformatics pipeline that integrates assembled and annotated Chinese hamster ovary (CHO) sequences with information derived from related organisms. We applied this pipeline to the analysis of CHO cells which were chosen as a model system owing to its relevance in the production of therapeutic proteins. Specifically, we analysed CHO cells undergoing butyrate treatment which is known to affect cell cycle regulation and to increase the specific productivity of recombinant proteins. By this means, we identified sequences for >13,000 CHO genes which added sequence information of approximately 5000 novel genes to the CHO model. More than 6000 transcript sequences are predicted to be complete, as they covered >95% of the corresponding mouse orthologs. Detailed analysis of selected biological functions such as DNA replication and cell cycle control, demonstrated the potential of NGS expression profiling in organisms without extended genome sequence to improve both data quantity and quality.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.