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: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: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: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:Seven Rambouillet-crossbred wethers were utilized to examine the impact of copper (Cu) supplementation on plasma, bile, liver, duodenum, jejunum, and ileum tissue Cu concentrations and Cu trafficking proteins abundance in the duodenum and liver. Wethers were blocked by body weight and assigned to one of two treatments: 1) control: no supplemental Cu and 2) +Cu: 12 mg of supplemental Cu/kg DM. After receiving treatments for 29 d, all wethers were transported to a USDA-inspected abattoir and harvested. Following harvest, blood, bile, liver, duodenum, jejunum, and ileum samples were collected for Cu concentration analysis. Additional duodenum and liver samples were collected for proteomic analysis.
Project description:We profiled lipids across multiple organs and biofluids from C57BL/6NCrl (B6NCrl-MVP) wild-type mice at two ages (16 and 92 weeks), including both sexes. Samples spanned the nervous (hippocampus, cerebrospinal fluid), connective (brown, subcutaneous, and visceral/abdominal fat), digestive (stomach, duodenum, jejunum, ileum, cecum, colon, liver, gallbladder), immune (spleen, thymus), reproductive (testes, uterus), excretory (kidney, bladder), endocrine (pancreas), cardiovascular (heart), muscular (quadriceps), and respiratory (lung) systems, plus biofluids (plasma, urine) and digestive products (feces). Lipidomics was performed by LC-MS/MS on a Thermo Scientific Orbitrap Exploris 240 coupled to a Vanquish UHPLC in both positive and negative ion modes. Analytes were separated on a Waters ACQUITY Premier BEH C18 column (50 x 2.1 mm, 1.7 um) prior to high-resolution MS acquisition.
Project description:We profiled polar metabolites across multiple organs and fluids from C57BL/6NCrl (B6NCrl-MVP) wild-type mice at two ages (16 and 92 weeks), including both sexes. Samples spanned the nervous (hippocampus, cerebrospinal fluid), connective (brown, subcutaneous, and visceral/abdominal fat), digestive (stomach, duodenum, jejunum, ileum, cecum, colon, liver, gallbladder), immune (spleen, thymus), reproductive (testes, uterus), excretory (kidney, bladder), endocrine (pancreas), cardiovascular (heart), muscular (quadriceps), and respiratory (lung) systems, plus biofluids (plasma, urine) and digestive products (feces). Polar metabolomics was performed by LC-MS/MS on a Thermo Scientific Q Exactive HF-X Quadrupole-Orbitrap coupled to a Vanquish UHPLC in positive mode. Metabolites were separated on a Waters ACQUITY Premier BEH Amide column (50 x 2.1 mm, 1.7 um) prior to high-resolution MS acquisition.
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: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.