dsRNA immunoprecipitation sequencing on a murine model of endotoxin-induced acute kidney injury
To investigate the extent of A-to-I RNA editing during endotoxemia in the kidney, we performed immunoprecipitation of dsRNA species, followed by stranded total RNA-seq on cytoplasmic and nuclear fractions of mouse kidneys. Overall design: C57BL/6J male mice were subjected to a single-dose, 4 mg/kg LPS (E. coli serotype 0111:B4) tail vein i.v. or vehicle saline in a volume of 300 ul. Kidney tissues were harvested at 0, 1, 4, 16, or 28 hours post-LPS injection, minced, and fractionated into cytoplasmic and nuclear compartments. Each fraction was immunoprecipitated using the anti-dsRNA monoclonal antibody J2 or IgG isotype control. cDNA library was prepared using the Clontech SMARTer Stranded Total RNA-Seq Kit v2.