|
| Status |
Public on Oct 02, 2013 |
| Title |
SR3-10/SR3-11 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
yeast cells harvested by the end of fermentation from brewery cylindro-conical vessel
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: HEBRU
run: 10
|
| Treatment protocol |
successive runs varied from 0 to 20, without run 14
|
| 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 cylindro-conical vessel
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: HEBRU
run: 11
|
| Treatment protocol |
successive runs varied from 0 to 20, without run 14
|
| 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 0 to run 20 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 |
Apr 10, 2013 |
| Last update date |
Oct 02, 2013 |
| Contact name |
Frank Stahl |
| E-mail(s) |
[email protected]
|
| 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 |
GPL16996 |
| Series (2) |
| GSE45946 |
Comparison between all runs of industrial serial repitching 3 |
| GSE45951 |
Serial industrial repitching and stress |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1120144_100_SR3-10-Fluorescein+SR3-11-Biotin_700-550.gpr.gz |
70.7 Kb |
(ftp)(http) |
GPR |
| GSM1120144_100_SR3-10-Fluorescein+SR3-11-Biotin_700.gpr.gz |
73.6 Kb |
(ftp)(http) |
GPR |
| GSM1120144_100_SR3-10-Fluorescein+SR3-11-Biotin_750-600.gpr.gz |
72.9 Kb |
(ftp)(http) |
GPR |
| GSM1120144_100_SR3-10-Fluorescein+SR3-11-Biotin_800-650.gpr.gz |
75.0 Kb |
(ftp)(http) |
GPR |
| GSM1120144_100_SR3-10-Fluorescein+SR3-11-Biotin_850-700.gpr.gz |
76.5 Kb |
(ftp)(http) |
GPR |
| GSM1120144_100_SR3-10-Fluorescein+SR3-11-Biotin_900-750.gpr.gz |
77.9 Kb |
(ftp)(http) |
GPR |
| GSM1120144_33_SR3-10-Fluorescein+SR3-11-Biotin_700-550.gpr.gz |
66.6 Kb |
(ftp)(http) |
GPR |
| GSM1120144_33_SR3-10-Fluorescein+SR3-11-Biotin_700.gpr.gz |
69.4 Kb |
(ftp)(http) |
GPR |
| GSM1120144_33_SR3-10-Fluorescein+SR3-11-Biotin_750-600.gpr.gz |
69.0 Kb |
(ftp)(http) |
GPR |
| GSM1120144_33_SR3-10-Fluorescein+SR3-11-Biotin_800-650.gpr.gz |
71.3 Kb |
(ftp)(http) |
GPR |
| GSM1120144_33_SR3-10-Fluorescein+SR3-11-Biotin_850-700.gpr.gz |
73.1 Kb |
(ftp)(http) |
GPR |
| GSM1120144_33_SR3-10-Fluorescein+SR3-11-Biotin_900-750.gpr.gz |
74.7 Kb |
(ftp)(http) |
GPR |
| Processed data included within Sample table |
