Project description:This SuperSeries is composed of the following subset Series: GSE31815: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Glucose at MID-log growth phase GSE31816: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + GLucose at transition-phase of growth (TS) GSE31817: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Galactose at MID-log growth phase GSE31818: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + galactose at transition-phase of growth (TS) Refer to individual Series
Project description:RNA sequencing was used to explore the expression of all genes in Streptococcus pneumoniae under heat stress. The pneumococcal strain 2/2 was grown in broth culture under control (37°C) and high temperature (40°C) conditions. 2/2 culture samples were taken at sequential time points and RNA was extracted and sequenced. Overall design: Streptococcus pneumoniae isolate 2/2 was cultured in seven 10 ml tubes of brain-heart infusion broth and incubated at 40°C + 5% CO2 for 6 h to mimic heat shock. The experimental control was the same isolate 2/2, also cultured in seven 10 ml tubes of brain-heart infusion broth but incubated at standard conditions of 37°C + 5% CO2. Broth cultures at five time points (2, 3, 4, 5 and 6 h of incubation) were removed and 19 ml of RNAprotect Bacteria Reagent (Qiagen) was added to stabilise the RNA. RNA was extracted from the samples using the Promega Maxwell® 16 Instrument and LEV simplyRNA Cells purification kit, following the manufacturer’s protocol. Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc) and sequencing was performed on the MiSeq (Illumina, Inc). The sequenced forward and reverse reads were paired and mapped to the S. pneumoniae strain 2/2 genome using Bowtie2 with the highest sensitivity option. Differential gene expression was analysed in Geneious version 9.1 (Biomatters Ltd) using the DESeq method. Genes with an adjusted p value <0.05 were considered to be differentially expressed.
Project description:This SuperSeries is composed of the following subset Series: GSE33033: ahrC mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine GSE33034: argR1 mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine GSE33035: argR1-ahrC mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine GSE33036: Streptococcus pneumoniae D39 wild-type grown in CDM+10 mM arginine compared to D39 wild type grown in CDM + 0.05 mM arginine Refer to individual Series
Project description:Using RNA sequencing to map differentially expressed genes in human brain microvascular endothelial cells challenged with Streptococcus pneumoniae or its ligand Adhesion lipoprotein.
Project description:Galactose promotes pneumococcal biofilms in vivo 15 mRNA profiles of Streptococcus pneumoniae samples that were grown under different conditions were generated using deep sequencing.
