Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
2008-02-08 | GSE10119 | GEO
Project description:Cyanobacteria-dominated microbial mat metatranscriptome from hot spring
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101
Project description:In Crohn’s disease (CD) pathology, we observed that: 1) a continuous process of fibrosis includes all the layers of the intestine as well as the surrounding mesenteric adipose tissue (MAT); 2) the amount of fibrosis in the MAT varies between samples even within a single case. To further investigate the molecular features of this fibrosis pattern, we did a paired study using formalin-fixed, paraffin-embedded blocks from ileocolonic resection specimens of seven CD patients. Specifically, one block contained ≥10% fibrosis amount while the other block contained <10% fibrosis amount within the MAT from the same case. MAT was selectively collected from serial histologic sections and total RNA was extracted for the Agilent Microarray analysis.
Project description:The aim of the current study was to characterize the differential cellular and exosomal miRNAs during inflammation or high fat diet-induced obesity in mice. Mesenteric adipose tissue (MAT) and abdominal aorta (AA) from mice fed a normal chow diet (NCD) or a high fat diet (HFD) were harvested for miRNA profiling. MAT-derived adipocytes (MAT-Ad) challenged with either lipopolysaccharide (LPS, 1 µg/ml) or PBS were harvested for miRNA profiling. Meanwhile, miRNAs encapsulated in MAT-Ad-derived exosomes (MAT-Ad-EX) were also analyzed. Hierarchical clustering analysis performed on most significantly regulated miRNAs (HFD vs NCD in tissues; LPS challenge vs PBS in the cells) showed a set of miRNAs that are differentially expressed in obese versus lean MAT or AA tissues, and in LPS-challenged versus PBS-treated MAT-Ads. The dysregulated of miRNAs in MAT-Ad-EX was also generated and hierarchically clustered, induced by prolonged exposure to microbial product.
Project description:The primary objective of the study was to investigate the uncoupling protein-1 (UCP1) associated features of human epicardial adipose tissue (eAT) using next generation deep sequencing. In addition, paired mediastinal adipose tissue (mAT) and subcutaneous adipose tissue (sAT) samples colleced from patients undergoing cardic surgeries at our center were included in the study.
Project description:Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determining the values of δ13C for different taxonomic divisions, and (ii) using those values as clues to the metabolic pathways employed by the respective organisms. This project measures >200 protein fractions and δ13C values for a sample of Cyanobacteria + Chloroflexi dominated microbial mat from Yellowstone National Park, USA.
Project description:in vitro comparison between two MRSA grown in rich (BHI) and poor media (SNM), compared with the nasal metatranscriptome reads of S. aureus. Global expression profile of two MRSA strains of S.aureus harvested in two different growth phases and compared with a metatranscriptome nose sample of a S. aureus carrier.
