|
| Status |
Public on Jul 18, 2014 |
| Title |
A2/A3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
yeast cells harvested by the end of fermentation from brewery A cylindro-conical vessel
|
| Organism |
Saccharomyces pastorianus |
| Characteristics |
strain: HEBRU
run: 2
pool: The RNA of 3 corresponding runs was pooled in an equimolar manner.
|
| Treatment protocol |
successive runs varied from 1 to 6
|
| Growth protocol |
Beer brewery process, industrial serial repitching
|
| Extracted molecule |
total RNA |
| 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.
|
| Label |
Cy3
|
| Label protocol |
The indirect labeling by the tyramide-signal-amplification method 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.
|
| |
|
| Channel 2 |
| Source name |
yeast cells harvested by the end of fermentation from brewery A cylindro-conical vessel
|
| Organism |
Saccharomyces pastorianus |
| Characteristics |
strain: HEBRU
run: 3
pool: The RNA of 3 corresponding runs was pooled in an equimolar manner.
|
| Treatment protocol |
successive runs varied from 1 to 6
|
| Growth protocol |
Beer brewery process, industrial serial repitching
|
| Extracted molecule |
total RNA |
| 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.
|
| Label |
Cy5
|
| Label protocol |
The indirect labeling by the tyramide-signal-amplification method 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.
|
| |
|
| |
| Hybridization protocol |
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 recommendations.
|
| Scan protocol |
The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.
|
| Description |
Gene expression of cells from run 1 to run 6 and a control samples, that consists of a pool of all RNAs from run 1-6, from brewery A was analyzed. Run 2 was used as alignment control.
|
| Data processing |
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.
|
| |
|
| Submission date |
Nov 14, 2013 |
| Last update date |
Jul 18, 2014 |
| Contact name |
Frank Stahl |
| E-mail(s) |
stahl@iftc.uni-hannover.de
|
| Phone |
0511-7622968
|
| Organization name |
Universität Hannover
|
| Department |
Institut für Technische Chemie
|
| Street address |
Callinstr. 3
|
| City |
Hannover |
| ZIP/Postal code |
30167 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17932 |
| Series (2) |
| GSE52378 |
Comparison between all runs of a serial repitching in brewery A |
| GSE52380 |
Comparison between brewery A and brewery B |
|
