Project description:Replicate cultres of Saccharomyces cerevisiae strain VL3 (a commercial wine strain) were inititaed with and without the the co-inoculation of a second yeast species, Pichia kluyveri (PKKR1). In addition replicate cultures of Pichia kluyveri were initiated. The media for all cultures was sterile Sauvignon blanc grape juice. Triplicates of each treatment were destructively harvested at days 2, 9 and 16 of fermentation and RNA extracted. RNA from S. cerevisiae could not be preferentially extracted from co-ferments. P. kluyveri genome has not been sequenced and so homology to S. cerevisiae probes on the array could not be accurately estimated. We extracted RNA from the P. kluyveri single ferments and hybridised them to the S. cerevisiae arrays to control for this. These species diverged over 100 MYA, and we did not observe abundant homology by way of cross hybridisation. The mean probe intensity for P. kluyveri cDNA was 17-fold lower than for S. cerevisiae, but some probes reported reasonable signal. The intensity distribution of these probes fit a log-normal distribution (P<0.01). 97% of the distribution fell below one-thirtieth of the S. cerevisiae maximum intensity: the remaining 3%, comprising 429 probes, potentially have reasonable homology to P. kluyveri cDNA and we removed these from all analyses. Please see associated additional file 'removePKKR1.r' R code to achieve this.
Project description:Array analysis of total RNA from mTECs 12 h post infection with influenza. Strains used were Mock, PR8, X31, VN6+2 (MOI 0.015) Time Point: 12 h post infection (Mock, PR8, X31, VN) MOI 0.015; in biological triplicates. Total samples: 12.
Project description:Array analysis of total RNA from mTECs 12 h post infection with influenza. Strains used were Mock, PR8, X31, VN6+2 (MOI 3) Time Point: 12 h post infection (Mock, PR8, X31, VN) MOI 3.0; in biological triplicates. Total samples: 12.
Project description:Array analysis of total lung RNA obtained from mice 12,16,24 h post infection with influenza. Strains used were Mock, PR8, X31, VN62 (1x10^5pfu) Time Point: 12, 16, 24 h post infection (Mock, PR8, X31, VN62); Mock group has three biological replicates, virally infected groups have nine replicates.
Project description:Array analysis of total lung RNA obtained from mice 12 h post infection with influenza. Strains used were Mock, PR8, X31, VN6+2 (1x10^5pfu) Time Point: 12 h post infection (Mock, PR8, X31, VN); Mock group has four biological replicates, virally infected groups have five replicates. Total samples: 19.
Project description:We used microarrays to analyse the global program of gene expression in response to Influenza A (X31) infection in lungs from C57BL/6 wt, 129S7 wt and IFNAR-/- (129) mice. Mock- or 5 day influenza A (X31)-infected total lungs from mice with the indicated genotypes were collected and processed for expression profiling.
Project description:To understand the Sef1-dependent gene expression in Lachancea kluyveri under both fermentative and respiratory conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type and sef1 deletion mutant under both YPD and YPGly conditions.
Project description:In the frame of a multispecies project, Lachancea kluyveri cells were treated with 5 mM sodium selenite. Cells were collected 10, 20, 30, 40, 50, 60, 70 and 80 minutes after the treatment and their transcriptomes were compared to those of mock-treated cultures. Four independent biological replicates were performed.
