article published yes Giselle T Cheung author 471195F6-F248-11E8-B48F-1D18A9856A870000-0001-8457-2572 Florian Pauler author 48EA0138-F248-11E8-B48F-1D18A9856A870000-0002-7462-0048 Peter Koppensteiner author 3B8B25A8-F248-11E8-B48F-1D18A9856A870000-0002-3509-1948 Simon Hippenmeyer author 37B36620-F248-11E8-B48F-1D18A9856A870000-0003-2279-1061 SiHi department PreCl department Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression project The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing. For complete details on the use and execution of this protocol, please refer to Cheung et al. 1 https://research-explorer.ista.ac.at/download/17232/18810/2024_STARProtoc_Cheung2.pdf application/pdfno Elsevier2024 eng 2666-1667 3896807610.1016/j.xpro.2024.103168 53 Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href="https://doi.org/10.1016/j.xpro.2024.103168">10.1016/j.xpro.2024.103168</a>. Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href="https://doi.org/10.1016/j.xpro.2024.103168">10.1016/j.xpro.2024.103168</a> Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href="https://doi.org/10.1016/j.xpro.2024.103168">https://doi.org/10.1016/j.xpro.2024.103168</a>. Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168. G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024. Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href="https://doi.org/10.1016/j.xpro.2024.103168">https://doi.org/10.1016/j.xpro.2024.103168</a> G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024). 172322024-07-14T22:01:10Z2025-12-30T10:54:12Z