Isolation of yeast and mammalian stress granule cores

•Stress granule cores are stable ex vivo.•Stress granule cores contain known stress granule components and RNA.•Stress granule cores are purified using a combination of centrifugation followed by immunoprecipitation.•A purified population of stress granule cores can be used for biochemical, proteomic, and transcriptomic experiments. Stress granules are dynamic, conserved RNA-protein (RNP) assemblies that form when translation is limiting; and are related to pathological aggregates in degenerative disease. Mammalian stress granules are comprised of two structures – an unstable shell and more stable cores. Herein we describe methodology for isolation of stress granule cores from both yeast and mammalian cells. The protocol consists of first enriching for stress granule cores using centrifugation and then further purifying stress granule cores using immunoprecipitation. The stress granule core isolation protocol provides a starting point for assisting future endeavors aimed at discovering conserved RNA regulatory mechanisms and potential links between RNP aggregation and degenerative disease.