The circadian transcriptome of mouse CD8+ T cells

To address the T cell-intrinsic rhythms underlying circadian variations of their functions, we analyzed gene expression rhythms in mouse CD8+ T cells. To do this, we entrained 8 weeks old male C57BL/6J mice for at least 2 weeks in a light:dark cycle, then put them in constant darkness (DD). Mice were sacrificed every 4 h over 48 h, on the second and third day in DD, and brachial, axillary and inguinal lymph nodes (LNs) were harvested. For each of the 12 time points, LNs from 6 mice were pooled. CD8+ T cells were isolated using EasySepTM mouse CD8a positive selection kit (STEMCELL technologies). The purity of the CD8 T cells was between 95.6 and 98.9% in all samples. Total RNA was extracted and RNA sequencing performed. Subsequent analysis aimed to identify transcript that show significant rhythmicity. Overall design: CD8+ T cells from 8 weeks old male C57BL/6J mice sacrificed at 12 circadian times over 2 days in constant darkness