Lb. brevis strains were grown in MRS broth supplemented or not with 5 % EtOH, 30 ppm iso-a-acids or adjusted to pH4. Cultures were grown at 30 degrees
Extracted molecule
total RNA
Extraction protocol
RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (Ainsworth, S.; Zomer, A.; Mahony, J.; van Sinderen, D. Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Applied environmental microbiology 2013, 79, 4786-4798, doi:10.1128/aem.01197-13).
Label
Cy3
Label protocol
Labelling was performed as described previously (Ainsworth, S.; Zomer, A.; Mahony, J.; van Sinderen, D. Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Applied environmental microbiology 2013, 79, 4786-4798, doi:10.1128/aem.01197-13).
Lb. brevis strains were grown in MRS broth supplemented or not with 5 % EtOH, 30 ppm iso-a-acids or adjusted to pH4. Cultures were grown at 30 degrees
Extracted molecule
total RNA
Extraction protocol
RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (Ainsworth, S.; Zomer, A.; Mahony, J.; van Sinderen, D. Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Applied environmental microbiology 2013, 79, 4786-4798, doi:10.1128/aem.01197-13).
Label
Cy5
Label protocol
Labelling was performed as described previously (Ainsworth, S.; Zomer, A.; Mahony, J.; van Sinderen, D. Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Applied environmental microbiology 2013, 79, 4786-4798, doi:10.1128/aem.01197-13).
Hybridization protocol
Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).
Scan protocol
Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).
Data processing
Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). Data processing DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 2-FL or 3-FL/sorbitol or lactose, or 2-FL or lactose/ribose ratios from a single array experiment.
