Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Spatial mapping of barcoded, brain-tropic AAVs using multiplexed RNA <i>in situ</i> hybridization.

Molecular therapy. Advances·2026
Same author

Interleukin-36 upregulates type-I interferon responses in systemic lupus erythematosus by promoting the accumulation of self-nucleic acids.

Frontiers in immunology·2026
Same author

Cell specific perfusion rates drive growth dynamics and metabolism in CHO N-1 perfusion processes independent of perfusion rate control method.

Frontiers in bioengineering and biotechnology·2025
Same author

Mapping administration route-dependent transduction profiles of commonly used AAV variants in mice by barcode amplicon sequencing.

Molecular therapy. Methods & clinical development·2025
Same author

Single-cell landscape of peripheral immune cells in MASLD/MASH.

Hepatology communications·2025
Same author

Prostate Cancer: De-regulated Circular RNAs With Efficacy in Preclinical <i>In Vivo</i> Models.

Cancer genomics & proteomics·2025

Related Experiment Video

Updated: Jun 15, 2026

Cost-Efficient Transcriptomic-Based Drug Screening
06:40

Cost-Efficient Transcriptomic-Based Drug Screening

Published on: February 23, 2024

Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing.

Fabian Birzele1, Jochen Schaub, Werner Rust

  • 1Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstrasse 67, 88397 Biberach an der Riss, Germany. fabian.birzele@boehringer-ingelheim.com

Nucleic Acids Research
|March 3, 2010
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing (NGS) enables expression profiling in organisms without prior genome data. This study developed a bioinformatics pipeline for Chinese hamster ovary (CHO) cells, identifying thousands of novel genes and improving data quality for therapeutic protein production.

More Related Videos

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
12:54

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Related Experiment Videos

Last Updated: Jun 15, 2026

Cost-Efficient Transcriptomic-Based Drug Screening
06:40

Cost-Efficient Transcriptomic-Based Drug Screening

Published on: February 23, 2024

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
12:54

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Next-generation sequencing (NGS) offers advanced capabilities for gene expression profiling and genome analysis.
  • Chinese Hamster Ovary (CHO) cells are crucial for producing therapeutic proteins, but lack comprehensive genomic data.
  • Butyrate treatment in CHO cells influences cell cycle regulation and recombinant protein productivity.

Purpose of the Study:

  • To demonstrate the feasibility of expression profiling in organisms lacking genome sequence information using NGS.
  • To develop and apply a novel bioinformatics pipeline for analyzing Chinese Hamster Ovary (CHO) cell transcriptomes.
  • To identify novel genes and improve sequence information in the CHO cell model.

Main Methods:

  • Utilized Illumina's mRNA-seq technology for expression profiling.
  • Developed a bioinformatics pipeline integrating assembled CHO sequences with data from related organisms.
  • Applied the pipeline to analyze CHO cells undergoing butyrate treatment.

Main Results:

  • Identified sequences for over 13,000 CHO genes, adding approximately 5000 novel genes to the CHO model.
  • Predicted over 6000 complete transcript sequences, covering >95% of mouse orthologs.
  • Detailed analysis of DNA replication and cell cycle control functions demonstrated improved data quantity and quality.

Conclusions:

  • NGS expression profiling is feasible in organisms without extensive genome sequences.
  • The developed bioinformatics pipeline enhances gene discovery and transcript completeness in CHO cells.
  • This approach improves the understanding of cellular functions and protein production in CHO models.