We report that Bi$_2$Se$_3$ thin films can be epitaxially grown on SrTiO$_{3}$ substrates, which allow for very large tunablity in carrier density with a back-gate. The observed low field magnetoconductivity due to weak anti-localization (WAL) has a very weak gate-voltage dependence unless the electron density is reduced to very low values. Such a transition in WAL is correlated with unusual changes in longitudinal and Hall resistivities. Our results suggest much suppressed bulk conductivity at large negative gate-voltages and a possible role of surface states in the WAL phenomena. This work may pave a way for realizing three-dimensional topological insulators at ambient conditions.