Response to the letter to editor for "concerns regarding the three-time-point sampling approach for diurnal transcriptome analysis in adipose tissue: evidence from fasting-independent time-of-day effects".

We respond to methodological concerns regarding the use of three daytime adipose tissue biopsies to estimate diurnal transcriptomic patterns. We clarify that the Stenvers et al. dataset was used for a technical evaluation of reduced temporal sampling, not as a biological replication of our dietary intervention. Additional analyses in healthy controls and participants with type 2 diabetes showed that rhythmic gene recovery was incomplete, particularly for weak oscillations. However, amplitude and acrophase estimates remained highly concordant among genes classified as rhythmic in both analyses. We also clarify that clock time, meal timing, and fasting duration were matched between interventions in our crossover study. Together, these findings support the reliability of our approach for robust diurnal signals and strengthen the interpretation of the diet-dependent transcriptomic changes directly observed in our study. We appreciate Chen's constructive comments, which allow us to clarify the scope and limitations of our approach.