Project description:Investigation of whole genome gene expression level changes in Yersinia intermedia strain ATCC 29909 in response to oxygen. The experiments and results have not been published yet (manuscript has been submitted to journal office and is under revision)
Project 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).
Project description:Investigation of whole genome gene expression level changes in Yersinia intermedia strain ATCC 29909 in response to oxygen. The experiments and results have not been published yet (manuscript has been submitted to journal office and is under revision) A 6 chip (whole-genome-tiled array) study using total RNA recovered from the following: 6 separate cultures of Yersinia intermedia strain ATCC 29909 grown in minimal medium with glucose (3 grown in the presence of oxygen and 3 grown without oxygen). Each whole-genome-tiled arrays contained ~320,000 probes representing 3953 genes that included 3887 protein coding genes (and 18 likely pseudogenes), 12 non-coding RNAs and 36 tRNAs. Data from probes corresponding to intergenic regions (and some pseudogenes, rRNA genes and unannotated genes) of the genome were not considered in the present analysis.