Slow oscillations in the sleeping and anesthetized brain invariantly emerge as an alternation between Up (high firing) and Down (almost quiescent) states. In cortex, they occur simultaneously in cell assemblies in different layers and propagate as traveling waves, a concerted activity at multiple scales whose interplay and role is still under debate. Slow oscillations have been reported to start in deep layers, more specifically in layer 5. Here, we studied the laminar organization of slow oscillations in the anesthetized rat cortex and we found that the activity leading to Up states actually initiates in layer 6, then spreads towards upper layers. Layer 5 cell assemblies have a threshold-like activation that can persist after layer 6 inactivation, giving rise to hysteresis loops like in "flip-flop" computational units. We found that such hysteresis is finely tuned by the columnar circuitry depending on the recent history of the local ongoing activity. Furthermore, thalamic inactivation reduced infragranular excitability without affecting the columnar activation pattern. We propose a role for layer 6 acting as a hub unraveling a hierarchy of cortical loops.