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We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation. Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp) Endow, Sharyn A.; Miller, Sara E.; Ly, Phuong Thao (2021). CIL:50673, Drosophila melanogaster. In Cell Image Library. UC San Diego Library Digital Collections. Dataset. https://doi.org/10.6075/J0542NRV