This data set is part of a larger data harmonization effort to make lake sediment core data machine readable and comparable. Here we standardized diatom count data of sediment core PG1984, retrieved in 2009 from Lake Sysy-Kyuele (Yakutia, Russia) at 2.4 m water depth. The thermokarst lake Sysy-Kyuele is situated in an exorheic basin in a coniferous forest area and has one outflow and no visible inflow. It lies at an elevation of ca. 73m a.s.l. with a surface area of ca. 1 km2 and a maximum lake water depth of estimated 2.5 m. The 1.2 m sediment core was retrieved by a UWITEC hammer action gravity corer during the RU-Land_2009_Lena-transect expedition of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI, Germany, Potsdam) in cooperation with the North Eastern Federal State University (NEFU, Russia, Yakutsk). Diatoms have been counted using a ZEISS light microsocope at 1000x magnification at AWI Potsdam.