Pathogen Gene Expression Profiling During Infection Using a Nanostring nCounter Platform.
NanoString nCounter is a recently developed platform that can make direct multiplexed measurement of gene expression using color-coded probe pairs (Geiss et al., Nat Biotechnol 26(3):317-325, 2008; Malkov et al., BMC Res Notes 2:80, 2009). We have found that this platform is uniquely suitable for quantification of pathogen gene expression during infection, where pathogen RNA comprises a tiny portion of total RNA isolated from the infected tissue. Here, we describe a protocol that we have successfully applied to a number of pathogens across multiple infection models, including both invasive and mucosal infection by Candida albicans, and lung infection by Aspergillus fumigatus and Cryptococcus neoformans.
Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, MI 200B, Pittsburgh, PA, 15213, USA.
Wenjie
W
Xu
Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA.
Norma V
NV
Solis
Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA.
Scott G
SG
Filler
Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, MI 200B, Pittsburgh, PA, 15213, USA. apm1@cmu.edu.
Aaron P
AP
Mitchell
D001232:Aspergillus fumigatus / Q000235:genetics / Q000472:pathogenicity; D002176:Candida albicans / Q000235:genetics / Q000472:pathogenicity; D003455:Cryptococcus neoformans / Q000235:genetics / Q000472:pathogenicity; D015966:Gene Expression Regulation, Fungal; D006801:Humans; D007239:Infections / Q000235:genetics* / Q000382:microbiology; D036103:Nanotechnology / Q000379:methods*; D012313:RNA / Q000235:genetics* / Q000302:isolation & purification
D012313:RNA
Gene expression; In vivo profiling; Infection; NanoString; Pathogen; RNA isolation