Project name: Streptococcus pneumoniae

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.

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: Medical

Last updated: 2017-09-12