Project description:In order to characterize duplication polymorphisms in Drosophila simulans, we applied comparative genome hybridization (CGH) using tiling arrays originally designed to cover the full euchromatic genome of its sister species D. melanogaster. We only used the ~900,000 probes in the tiling arrays that had a perfect and unique match to the D. simulans genome (droSim1). We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates. The probabilities of mutation were parsed to make duplication calls. The supplementary file linked to each Sample record contains for each probe, its location in the D. simulans genome and its posterior probability of being duplicated (output from the Hiddem Markov Model)

2011-09-01 | GSE29260 | GEO

Detection of duplication polymorphisms in the Drosophila simulans genome

2011-08-31 | E-GEOD-29260 | biostudies-arrayexpress

Influence of Staphylococcus aureus strain background on Sa3 phage life cycle switches

Project description:Staphylococcus aureus (S. aureus) is a known pathogen able to infect humans and animals. Human S. aureus isolates are often associated with carriage of Sa3int prophages combined with loss of beta-hemolysin production due to gene disruption, whereas animal isolates are positive for beta-hemolysin associated with absence of Sa3int prophages. Sa3int prophages are known to contribute to staphylococcal fitness and virulence in human host by providing human-specific virulence factors encoded on the prophage genome. Strain-specific differences in regard to phage transfer, lysogenization and induction are attributable to yet unknown staphylococcal factors specifically influencing prophage gene expression. In this work we used tagRNA-sequencing approach to specifically search for these unknown host factors and differences in prophage gene expression. For this purpose, we established a workflow revealing the first direct comparison for differential gene expression analysis on two distinct single-lysogenic S. aureus isolates. Further, global gene expression patterns were investigated in two S. aureus isolates upon mitomycin C treatment and compared to uninduced conditions. This provides new insights into the tightly linked host-phage interaction network.

2022-10-03 | GSE214523 | GEO

Corynebacterium simulans strain:1B08

Project description:Corynebacterium simulans strain:1B08 Genome sequencing and assembly

| PRJNA279605 | ENA

Drosophila simulans strain:w501

Project description:Drosophila simulans strain:w501 Genome sequencing and assembly

| PRJNA170244 | ENA