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).

2016-09-19 | E-MTAB-5062 | biostudies-arrayexpress

Expression analysis of Yersinia intermedia strain ATCC 29909 at 28 C in minimal medium with glucose under aerobic and anaerobic conditions

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.

2013-08-21 | E-GEOD-50043 | biostudies-arrayexpress

Yersinia kristensenii strain:Y231

Project description:Yersinia kristensenii strain:Y231 Genome sequencing

| PRJNA240099 | ENA

A proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163

Project description:Oenococcus oeni is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines. O. oeni possesses an array of metabolic activities which can modify the taste and aromatic properties of wine. There is therefore industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the O. oeni ATCC BAA-1163 proteome. Total and membrane protein preparations from O. oeni were standardized and analyzed by two-dimensional gel electrophoresis. Using tandem mass spectrometry we identified 226 different polypeptides corresponding to 155 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.

2014-04-16 | PXD000579 | Pride

Oceanimonas smirnovii ATCC BAA-899

Project description:Oceanimonas smirnovii ATCC BAA-899

| PRJNA185294 | ENA

Caldimonas manganoxidans ATCC BAA-369

Project description:Caldimonas manganoxidans ATCC BAA-369

| PRJNA182454 | ENA

Colwellia piezophila ATCC BAA-637

Project description:Colwellia piezophila ATCC BAA-637

| PRJNA182419 | ENA

Enterobacter kobei ATCC BAA-260 isolate:ATCC BAA-260

Project description:Enterobacter kobei ATCC BAA-260 genome sequencing