normalization data transformation protocol
Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized by the median of the background intensities and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes. ID_REF = VALUE = The values are normalized log2 Cy5/Cy3 F635 Median = B635 = F532 Median = B532 = Flags =
array scanning protocol
The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.
The differently labeled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C, overnight) simultaneously in one experiment to the same array according to the slide manufacturer´s and Micromax TSA Kit recommendations.
The indirect labeling by the tyramide-signal-amplification method (MicromaxTM TSATM labeling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy3/Cy5 signals of microarray detection. 6 µg of the total RNA were reverse transcribed and thereby the cDNA was labeled with Fluorescein-dCTP/ Biotin-dCTP.
Beer brewery process, industrial serial repitching
sample treatment protocol
successive runs varied from 4 to 22
nucleic acid extraction protocol
The isolation of RNA was done by disruption of the cells under liquid nitrogen using mortar and pistil and then the Qiagen RNeasy Midi Kit with some modifications within the manufacturers´ protocol and the Qiagen RNase-Free DNase Set were applied.