E-MTAB-5062 - RNA-seq analysis of Helicobacter cinaedi ATCC BAA-847 under microaerobic and aerobic culture conditions

Status
Last updated on 19 September 2016, released on 19 September 2016
Organism
Helicobacter cinaedi CCUG 18818 = ATCC BAA-847
Samples (39)
Protocols (6)
Description
Helicobacter cinaedi is an emerging bacterial pathogen of immunosuppressed individuals. The species is traditionally thought to require an H2-enhanced microaerobic atmosphere for growth, although it can proliferate under aerobic conditions when co-cultured with epithelial monolayers or supplemented with certain metabolites (notably, L-lactate). The goal of this experiment was to assess the global transcription changes that occur in the H. cinaedi type strain (ATCC BAA-847) under various media and atmospheric conditions. These include bacterial monoculture, as well as co-culture with Caco-2 intestinal epithelial cells. In total, Illumina mRNA-seq (stranded, paired-end) was performed on H. cinaedi grown under 9 in vitro culture conditions (4-5 biologic replicates per condition).
Experiment type
RNA-seq of coding RNA 
Contacts
Citation
Epithelial Co-Culture and L-Lactate Promote Growth of Helicobacter cinaedi under H2-free Aerobic Conditions. Jonathan E. Schmitz, Takako Taniguchi, Naoaki Misawa, and Timothy L. Cover. Applied and Environmental Microbiology  (2016), PMID:27613684
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-5062.idf.txt
Sample and data relationshipE-MTAB-5062.sdrf.txt
Processed data (2)E-MTAB-5062.processed.1.zip, E-MTAB-5062.processed.2.zip
Links