This detailed book compiles state-of-the-art protocols from researchers actively working in the area of autophagy, a crucial cellular process that regulates numerous cellular functions. In order to accelerate advances in the field, the volume explores aspects of autophagy research where a better understanding of its role is vitally important, such as in the maintenance of stem cell subpopulations and the regulation of differentiation. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.