PT - JOURNAL ARTICLE AU - Subashika Govindan AU - Polina Oberst AU - Denis Jabaudon TI - <em>In vivo</em> pulse-labeling of isochronic cohorts of cells in the central nervous system using FlashTag AID - 10.1101/286831 DP - 2018 Jan 01 TA - bioRxiv PG - 286831 4099 - http://biorxiv.org/content/early/2018/03/22/286831.short 4100 - http://biorxiv.org/content/early/2018/03/22/286831.full AB - This protocol describes a fluorescence birthdating technique to label, track and isolate isochronic cohorts of newborn cells in the central nervous system in vivo. Injection of carboxyfluorescein esters into the cerebral ventricle allows pulse-labeling of M-phase progenitors in touch with the ventricle and their progeny across the central nervous system, a procedure we termed FlashTag. Labeled cells can be imaged ex vivo or in fixed tissue, targeted for electrophysiological experiments, or isolated using Fluorescence-Activated Cell Sorting (FACS) for cell culture or (single-cell) RNA-sequencing. The dye is retained for several weeks, allowing labeled cells to be identified postnatally. This protocol describes the labeling procedure using in utero injection, the isolation of live cells using FACS, as well as the processing of labeled tissue using immunohistochemistry.