Differential gene and transcript expression analysis of RNA-seq

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim, David R Kelley, Harold Pimentel, Steven L Salzberg, John L Rinn and Lior Pachter: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 2012,  7, 562-578.

Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and […]

The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids

Video Article Published on JoVE

Rothschild DE, Srinivasan T, Aponte-Santiago LA, Shen X, Allen IC : JoVE 111, (2016) doi:10.3791/54033, Published 18 May 2016

This protocol has been generated to outline a simple procedure to culture and treat small intestinal organoids with microbial pathogens and pathogen associated molecular patterns (PAMPs). It also emphasizes the normalization techniques […]

Highly Multiplexed Simultaneous Detection of RNAs and Proteins

Highly multiplexed simultaneous detection of RNAs and proteins in single cells

Andreas P Frei, Felice-Alessio Bava, Eli R Zunder, Elena W Y Hsieh, Shih-Yu Chen, Garry P Nolan & Pier Federico Gherardini: Nature Methods 2016 Jan; 269-275. Published online 2016 January 25. doi:10.1038/nmeth.3742.

This method combines the Flow cytometry possibility to acquire single cell expression […]

By |November 30th, 2016|Categories: Laboratory Techniques, Protocols||0 Comments

Advanced CUBIC protocols for whole-brain and

Advanced CUBIC Protocols for Whole-Brain and Whole-Body Clearing and Imaging

Etsuo A Susaki, Kazuki Tainaka, Dimitri Perrin, Hiroko Yukinaga, Akihiro Kuno and Hiroki R Ueda: Advanced CUBIC Protocols for Whole-Brain and Whole-Body Clearing and Imaging. Nature protocols 2015, 10: 1709-1727.

This protocol describes in detail how to perform advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and […]

An Introduction to Saccharomyces Cerevisia

JoVE Science Education Database. Model Organisms I: yeast, Drosophila and C. elegans. An Introduction to Saccharomyces cerevisiae. Journal of Visualized Experiments, Cambridge, MA, doi: 10.3791/5081 (2014).

Saccharomyces cerevisiae (commonly known as baker’s yeast) is a single-celled eukaryote that is frequently used in scientific research. S. cerevisiae is an attractive model organism due to the fact […]

By |June 3rd, 2014|Categories: Laboratory Techniques||0 Comments

An Introduction to the Laboratory Mouse: Mus Musculus

JoVE Science Education Database. Model Organisms II: Mouse, Zebrafish, and Chick. An Introduction to the Laboratory Mouse: Mus musculus. Journal of Visualized Experiments, Cambridge, MA, doi: 10.3791/5129 (2014).

Mice (Mus musculus) are an important research tool for modeling human disease progression and development in the lab. Despite differences in their size and appearance, mice share […]

By |June 3rd, 2014|Categories: Laboratory Techniques||0 Comments

An Introduction to the Zebrafish: Danio Rerio

JoVE Science Education Database. Model Organisms II: Mouse, Zebrafish, and Chick. An Introduction to the Zebrafish: Danio rerio. Journal of Visualized Experiments, Cambridge, MA, doi: 10.3791/5128 (2014).

Zebrafish (Danio rerio) are small freshwater fish that are used as model organisms for biomedical research. The many strengths of these fish include their high degree of genetic […]

By |June 3rd, 2014|Categories: Laboratory Techniques||0 Comments

An Introduction to Transfection

JoVE Science Education Database. Basic Methods in Cellular and Molecular Biology. An Introduction to Transfection. Journal of Visualized Experiments, Cambridge, MA, doi: 10.3791/5068 (2014).

Transfection is the process of inserting genetic material, such as DNA and double stranded RNA, into mammalian cells. The insertion of DNA enables the expression, or production, of proteins using the […]

By |June 3rd, 2014|Categories: Laboratory Techniques||0 Comments

An Introduction to Working in the Hood

JoVE Science Education Database. General Laboratory Techniques. An Introduction to Working in the Hood. Journal of Visualized Experiments, Cambridge, MA, doi: 10.3791/5036 (2014).

Hoods are a common class of instrument, which act as a protective enclosure for various types of laboratory experiments. They serve to shield experimental samples from the environment, as well as to […]

By |June 3rd, 2014|Categories: Laboratory Techniques||0 Comments

An Introduction to the Chick: Gallus Gallus Domesticus

JoVE Science Education Database. Model Organisms II: Mouse, Zebrafish, and Chick. An Introduction to the Chick: Gallus gallus domesticus. Journal of Visualized Experiments, Cambridge, MA, doi: 10.3791/5153 (2014).

The chicken embryo (Gallus gallus domesticus) is an extremely valuable model organism for research in developmental biology, in part because most of their development takes place within […]

By |June 3rd, 2014|Categories: Laboratory Techniques||0 Comments