|
| Status |
Public on Nov 14, 2011 |
| Title |
Environmental sample D10_12 (Myk6) |
| Sample type |
RNA |
| |
|
| Source name |
Environmental sample (pine forest soil)
|
| Organism |
soil metagenome |
| Characteristics |
sample type: pine forest soil microorganisms
sample_id: D10_12
geographical location: near Bayreuth, Germany (49°58'16'' N, 11°34'51'' E and 460 m alt.)
rna sample dilution used in hybn: 1:25 dilution of labelled RNA
|
| Treatment protocol |
none
|
| Growth protocol |
Samples were harvested from pine forest soil near Bayreuth, Germany (49°58'16'' N, 11°34'51'' E and 460 m alt.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were extracted as described in Peršoh et al. (2008), J. Microbiol. Meth. 75:19-24
|
| Label |
Cy5
|
| Label protocol |
1.5 µg total RNA was labelled using the CyScribe Drect mRNA Labelling Kit (GE Healthcare); total volume was 11 µl.
|
| |
|
| Hybridization protocol |
1 µl of a 1:25 dilution of labelled RNA were combined with Agilent's blocking agent and hybridization buffer (total 50 µl) and hybridized to one subarray
Labelled RNA samples (1 µl) were added directly and in a fivefold dilution to the Agilent's Gene Expression Hybridisation Solution; hybridisation was carried out at 65°C for 18 hours in an Agilent's hybridisation oven; microarrays were washed with Agilent's Wash Buffer Kit; Ozone-mediated Cy5 degradation was inhibited by applying Agilent's Stabilisation and Drying Solution.
|
| Scan protocol |
Microarrays were scanned using a FLA8000 scanner (Fuji) at 5 µm resolution and confocal signal capturing mode
|
| Description |
Myk6
Two independent samples (11 and 12) taken at the same sampling site
|
| Data processing |
Spot intensities were quantified using ArrayVision software (GE Healthcare) and values were calculated as background-corrected, artefact-removed volume per spot; spot segmentation was allowed to correct for different spot morphologies. Cy5 values were normalized to Cy3 values using the signal ratio (Cy3/Cy5) of Eukarya SSU rRNA probe signals present in four replicates on each subarray (Note: Cy3 values remained unchanged; they are identical to the background corrected raw values).
Probes such as internal controls were filtered out and will not appear in the associated publication. In the publication only the 11.3 k probes will be discussed and, therefore, only these probes are presented in the data table.
|
| |
|
| Submission date |
Mar 17, 2011 |
| Last update date |
Nov 14, 2011 |
| Contact name |
Alfons R Weig |
| E-mail(s) |
a.weig@uni-bayreuth.de
|
| Organization name |
University of Bayreuth
|
| Department |
Genomics and Bioinformatics
|
| Street address |
Universitaetsstrasse 30
|
| City |
Bayreuth |
| ZIP/Postal code |
95447 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13295 |
| Series (1) |
| GSE28018 |
A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity |
|
