Comparative transcriptome data of multi tissues in response to different environmental light-dark cycles

It is well known that host-microbes and immunity interactions are influenced by dietary patterns, as well as daily environmental light-dark (LD) cycles that entrain circadian rhythms in the host. Emerging data has highlighted the importance of diet patterns and timing on the interaction among circadian rhythms, gut microbiome, and immunity, however, their impacts on LD cycles are less reported. Therefore, we aim to study how LD cycles regulate the homeostatic crosstalk between gut microbiome, hypothalamic and hepatic circadian clock oscillations and immunity. We hypothesized that different environmental LD cycles: (1) constant darkness, LD0/24; (2) short light, LD8/16; (3) normal LD cycle, LD12/12; (4) long light, LD16/8; and (5) constant light, LD24/0, may affect immunity and metabolism to varying degrees. Therefore, 240 mice were managed with chow diets (CD) and antibiotics treatments (ABX) under five different LD cycles for 42 days. The liver (LIV), hypothalamus (HYP), inguinal white adipose tissue (iWAT), ileum epithelium (ILE), colon epithelium (COL), jejunum epithelium (JEJ), cecum epithelium (CEC), spleen (SPL), mammary gland (MAG), and thymus gland (THY) tissues were obtained for studying their impacts immunity using RNA-Seq data.众所周知，宿主-微生物（host-microbes）与免疫的相互作用受饮食模式调控，同时也受调控宿主昼夜节律（circadian rhythms）的日常环境明暗（light-dark, LD）周期影响。现有新兴研究已凸显饮食模式与饮食时机在昼夜节律、肠道菌群（gut microbiome）与免疫三者互作中的关键作用，但此类因素对LD周期的影响却鲜有报道。因此本研究旨在探究LD周期如何调控肠道菌群、下丘脑与肝脏的昼夜节律钟振荡，以及免疫之间的稳态串扰（homeostatic crosstalk）。我们提出如下假说：五种不同的环境LD周期，即（1）持续黑暗（LD0/24）、（2）短光照（LD8/16）、（3）正常LD周期（LD12/12）、（4）长光照（LD16/8）以及（5）持续光照（LD24/0），会在不同程度上影响机体免疫与代谢。为此，我们将240只小鼠分为两组，分别喂食标准饲料（chow diets, CD）与抗生素处理（antibiotics treatments, ABX），并在五种不同的LD周期下饲养42天。我们采集了肝脏（liver, LIV）、下丘脑（hypothalamus, HYP）、腹股沟白色脂肪组织（inguinal white adipose tissue, iWAT）、回肠上皮（ileum epithelium, ILE）、结肠上皮（colon epithelium, COL）、空肠上皮（jejunum epithelium, JEJ）、盲肠上皮（cecum epithelium, CEC）、脾脏（spleen, SPL）、乳腺（mammary gland, MAG）以及胸腺（thymus gland, THY）组织，并通过RNA测序（RNA-Seq）数据探究上述LD周期对免疫的影响。