Harvesting Alveolar Macrophages from the Mouse

Harvesting Alveolar Macrophages from the Mouse Using Lung Lavage

Chavez-Santoscoy AV, Huntimer LM, Ramer-Tait AE, Wannemuehler M, Narasimhan B: Harvesting murine alveolar macrophages and evaluating cellular activation induced by polyanhydride nanoparticles. Journal of visualized experiments : JoVE 2012(64):e3883.

Biodegradable nanoparticles have emerged as a versatile platform for the design and implementation of new intranasal vaccines against […]

By |March 15th, 2017|Categories: Protocols, Publications, Respiratory System||0 Comments

Murine Model of DSS-induced Acute Colitis

Murine Model of DSS-induced Acute Colitis

J Vis Exp. 2012 Feb 1;(60). pii: 3678. doi: 10.3791/3678. Investigating intestinal inflammation in DSS-induced model of IBD. Kim JJ1, Shajib MS, Manocha MM, Khan WI. 

Inflammatory bowel disease (IBD) encompasses a range of intestinal pathologies, the most common of which are ulcerative colitis (UC) and Crohn’s Disease (CD). Both UC […]

By |February 27th, 2017|Categories: Gastrointestinal System, Protocols, Publications||0 Comments

Airway Hyperresponsiveness in Murine Tracheal Rings

Assessment of Airway Hyperresponsiveness in Murine Tracheal Rings. Methods Mol Biol. 2013;1032:257-69. doi: 10.1007/978-1-62703-496-8_20.

Isolated tracheal rings have often been used to directly measure the contractile output of airway smooth muscle (ASM). Here, we describe the method for excising murine tracheas, mounting tracheal rings in organ baths, and measuring the isometric forces generated by the ASM when […]

By |February 12th, 2017|Categories: Protocols, Respiratory System||0 Comments

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 […]

Sequencing and cloning of antigen-specific antibodies from mouse memory B cells

Published in Nature Protocols

Lotta von Boehmer, Cassie Liu, Sarah Ackerman, Alexander D Gitlin, Qiao Wang, Anna Gazumyan & Michel C Nussenzweig :Nature Protocols 11, 1908-1923 (2016) doi:10.1038/nprot.2016.102, Published online 15 September 2016

Methods to identify genes encoding immunoglobulin heavy and light chains from single B lymphocytes vary in efficiency, error rate and practicability. Here we describe […]

High-resolution 3D analysis of mouse small-intestinal stroma

Published in Nature Protocols

Jeremiah Bernier-Latmani & Tatiana V Petrova :Nature Protocols 11, 1617–1629 (2016) doi:10.1038/nprot.2016.092, Published online 11 August 2016

Here we detail a protocol for whole-mount immunostaining of mouse small-intestinal villi that can be used to generate high-resolution 3D images of all gut cell types, including blood and lymphatic vessel cells, neurons, smooth muscle […]

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

Human Norovirus Culture in B Cells

Human norovirus culture in B cells

Melissa K Jones, Katrina R Grau, Veronica Costantini, Abimbola O Kolawole, Miranda de Graaf, Pamela Freiden, Christina L Graves, Marion Koopmans, Shannon M Wallet, Scott A Tibbetts, Stacey Schultz-Cherry, Christiane E Wobus, Jan Vinjé & Stephanie M Karst: Nat Protoc. 2015 Dec; 10(12): 1939-47. Published online 2015 Oct 29. […]

By |November 23rd, 2016|Categories: Protocols, Publications||0 Comments

Comparison of cell counting methods

Comparison of cell counting methods in rodent pulmonary toxicity studies: automated and manual protocols and considerations for experimental design

Patti C. Zeidler-Erdely, James M. Antonini, Terence G. Meighan, Shih-Houng Young, Tracy J. Eye, Mary Ann Hammer & Aaron Erdely (2016) Comparison of cell counting methods in rodent pulmonary toxicity studies: automated and manual protocols and […]