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. Overall design: Firstly, two hundreds and forty 10-week-old C57BL/6N murine line were selected and supplied, all mice were initially maintained under the same standard laboratory conditions to harmonize the environment and diets. The initial body weight of each mouse was 19-20 g. After acclimatization for 7 days, the mice were then randomly divided into following two parts: chow diets parts (CD, n = 120), and antibiotics treatment parts (ABX, n = 120). Adequate sterilized drinking water and pelleted feed (irradiation by Co60) were provided for CD mice, and the diets were consisted of corn, soybean, wheat, chicken and fish meal, vegetable oil, and a variety of customized vitamins and trace elements. Mice from ABX parts received same sterilized feed but added a cocktail of broad-spectrum antibiotics in their drinking water.Then, all 240 mice from CD and ABX parts were randomly divided into 10 groups to receive following 5 light-dark cycles : (1) 0 h light/24 h dark fed with CD (CD_LD0/24, n = 24); (2) 8 h light/16 h dark fed with CD (CD_LD8/16, n = 24); (3) 12 h light/12 h dark fed with CD (CD_LD12/12, n = 24); (4) 16 h light/8 h dark fed with CD (CD_LD16/8, n = 24); (5) 24 h light/0 h dark fed with CD (CD_LD24/0, n = 24); (6) 0 h light/24 h dark fed with ABX (ABX_LD0/24, n = 24); (7) 8 h light/16 h dark fed with ABX (ABX_LD8/16, n = 24); (8) 12 h light/12 h dark fed with ABX (ABX_LD12/12, n = 24); (9) 16 h light/8 h dark fed with ABX (ABX_LD16/8, n = 24); and (10) 24 h light/0 h dark fed with ABX (ABX_LD24/0, n = 24). Each mouse was maintained in a single cage in an environmentally controlled warehouse that allowed for manipulating light-dark cycles according to regulations, and light-dark cycles were controlled with an LED light strip of 150 to 200 lx and a temperature of 4500 to 5000 K, with the lights being turned off for 24 h of LD0/24; the lights being turned on at CT6 (defined as ZT0) and turned off at ZT8 of LD8/16; the light being turned on at ZT0 and turned off at ZT12 of LD12/12; the light being turned on at ZT0 and turned off at ZT16 of LD16/8; and the lights being turned on for 24 h of LD24/0. The trough, drinking fountain, and litter were changed every day after the lights were turned on at ZT0. Temperature within the warehouse was 22-24 °C, relative humidity was 55-65%, and negative pressure ventilation was used. The experimental lasted for 42 days and was under strict environmental control conditions.