Sleep fragmentation chamber

For sleep fragmentation experiments, female mice were placed in
a sleep fragmentation chamber (Lafayette Instrument, Lafayette, IN,
USA). The sweep bar moved along the bottom of the cage every 2 minutes
during the light cycle (Zeitgeber time 0–12). The sweep bar
automatically shut off and was stationary during the dark cycle
(Zeitgeber time 12–24). Control mice receiving undisturbed sleep
were placed in sleep fragmentation chambers with stationary sweep bars.
For bone marrow transplantation experiments, mice were placed in sleep
fragmentation cages 2–4 weeks after the transplant.

For sleep fragmentation studies, mice were placed in a sleep fragmentation chamber (Lafayette Instrument, Lafayette, IN) at the same time as initiation of special diet feeding. The sweep bar moved along the bottom of the cage every 2 minutes during the light cycle (ZT0–12). The sweep bar automatically shut off and was stationary during the dark cycle (ZT12–24). Control mice that received undisturbed sleep were placed in sleep fragmentation chambers with stationary sweep bars. For the control experiment in Extended Data Figure 1f-h, the sweep bar moved along the bottom of the cage every 2 minutes during the dark cycle (ZT12–0) and automatically shut off and was stationary during the light cycle (ZT0–12)