Project description:Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to study the pre-weaned lamb proteome and metaproteome in ten different gastrointestinal tracts: rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum.
Project description:C57BL/6Crl mice were fed 10 mg/kg BA or control for 13 days. Samples collected on day 14. Treatment groups included serocholate, serine + cholate, phenylalanocholate, phenylalanine + cholate, taurocholate, taurine + cholate, and a mock control.
Fecal, F; Colon, CL; Cecum, CE; Duodenum, DD; Gallbladder, GB; Ileum, IL; Liver, L
Project description:To understand how cholera toxin (CT) produced by Vibrio cholerae modulates gene expression of this organism within the intestine, RNA-seq analysis was performed on two samples each of WT and the ∆ctx mutant bacteria harvested from either the infant rabbit ileum or the cecum one-day post-intragastric infection. We found that 243 genes that were significantly up-regulated in the WT compared to the ∆ctx mutant and these included 101 genes in ileum samples, 118 in the cecum samples, and 24 in both samples. We found that genes known to be induced under low-iron growth conditions were up-regulated in WT relative to the ∆ctx mutant in both the ileum and in the cecum, with a marked up-regulation in the ileum relative to the cecum. We also found that genes involved in TCA cycle metabolism, L-Lactate utilization, and LCFA utilization were significantly up-regulated in the WT in the ileum relative to the ∆ctx mutant during infection. We conclude that CT-induced disease creates an iron-depleted metabolic niche in the gut that modulates the transcriptional profile of this pathogen during infection.
2019-07-31 | GSE132653 | GEO
Project description:Bacterial microflora of the Chicken Gut - Ileum, Cecum Metagenome
Project description:Copy number variation profiles comparing control female Dehong chiken blood DNA with 11 different chicken breeds(Silkie, Tibetan Chicken, Gallus gallus spadiceus, Bearded Chicken, Jinhu Chicken, Anak Chicken, Beijing Fatty Chicken, Langshan Chicken, Qingyuan partridge Chicken, Shek-Ki Chicken, Wenchang Chicken) blood DNA. Each test breeds had one male and one female sample, totally 22 test DNA samples.Goal is to get the golbal copy number variation profile between chicken breeds.
Project description: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.
Project description:Enteroendocrine cells (EECs) are the source of a variety of gut hormones that control local intestinal functions such as gallbladder contraction, pancreatic enzyme secretion and intestinal motility, as well as peripheral nutrient metabolism and appetite. This study aimed to map human EECs isolated from organoids derived from duodenum and ileum using single-cell RNA sequencing.
Project description:Results of RNA-seq of normal C57BL/6 small intestinal epithelial cells sorted from duodenum, jejunum and ileum separately. Samples are named as follow; mouse replicate number-duodenum(1), jejunum(2) or ileum(3). For example, 1-1, 1-2 and 1-3 representing duodenum, jejunum and ileum respectively from mouse replicate number 1.
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues from horses We generated DNA methylation data from n=333 horse tissue samples representing tissues. Blood samples were collected via venipuncture into EDTA tubes from across 24 different horse breeds (buffy coat). The other tissues were collected at necropsy. The tissue atlas was generated from two Thoroughbred mares as part of the FAANG initiative 37, with the following tissues profiled: adipose (gluteal), adrenal cortex, blood (PBMCs; only n=1 mare), cartilage (only n=1 mare), cecum, cerebellum (2 samples each from lateral hemisphere and vermis), frontal cortex, duodenum, fibroblast, heart (2 samples each from the right atrium, left atrium, right ventricle, left ventricle), hypothalamus, ileum, jejunum, keratinocyte, kidney (kidney cortex and medulla), lamina, larynx (i.e. cricoarytenoideus dorsalis muscle), liver, lung, mammary gland, mitral valve of the heart, skeletal muscle (gluteal muscle and longissimus muscle), occipital cortex, ovary, parietal cortex, pituitary, sacrocaudalis dorsalis muscle, skin, spinal cord (C1 and T8), spleen, suspensory ligament, temporal cortex, tendon (deep digital flexor tendon and superficial digital flexor tendon), uterus.
Project description:The aim of the project is to generate a peptidomics map of gut hormone peptides along the gastrointestinal tract, starting with the stomach and including the duodenum, jejunum, ileum, colon and rectum. The tissues would be collected after surgery and the peptide fraction extracted and anlysed by nano LC-MS to identify what peptide hormones are present. These data will then be used to compare against the murine transcriptome, and also for comparison against equivent peptides from human intestinal extracts.