|
| Status |
Public on Jun 15, 2012 |
| Title |
Monokaryon2_4-39_biological-replication_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
strain 4-39, monokaryon
|
| Organism |
Schizophyllum commune |
| Characteristics |
developmental stage: monokaryon
strain(s): 4-39
mating type loci: A1,1; B3,2
stage of clamp formation: no clamps
|
| Treatment protocol |
Mycelium was harvested, frozen in liquid nitrogen and ground with mortar and pestle to a powder.
|
| Growth protocol |
The S. commune strains were grown on solid medium (CYM) at 28°C. Mycelium of a mating interaction was transferred onto a cellophane membrane onto fresh CYM plates and grown for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from < 100 mg tissue powder using “Qiagen Rneasy plant mini kit” (Qiagen, Hilden, Germany), quality controlled with Agilent 2100 Bioanalyzer, using RNA 6000 Nano Kit, and a NanoDropTM 1000 Spectrophotometer (Thermo Scientific).
|
| Label |
biotin
|
| Label protocol |
For each array 1 µg of total RNA was labeled using the MassageAmpTM-Biotin Enhanced RNA Kit from Ambion.
|
| |
|
| Hybridization protocol |
Hybridization was done automatically over night (16 hours) at 45°C using RT-Analyzer from febit. The biotin labeling was detected with streptavidinphycoerythrin (SAPE), in combination with Consecutive Signal Enhancement (CSE) procedure from febit.
|
| Scan protocol |
The feature recognition, using Cy3 filter set, and signal calculation were done automatically within milliseconds using the Geniom RT Analyzer.
|
| Description |
blanks (only one single “T” nucleotide) are used for background corrections
|
| Data processing |
Background correction was performed using the intensities of blank probes which consist only of one single ”T” nucleotide. The median background intensity was subtracted from spot intensity. After converting any negative values to a low positive value (7), signal intensities were log2-transformed. The obtained data were processed using quantile normalization, and duplicate spots were averaged.
By R and Bioconductor computed log2 transformed and quantil normalized signal intensity
|
| |
|
| Submission date |
Jan 03, 2011 |
| Last update date |
Jun 15, 2012 |
| Contact name |
Erika Kothe |
| E-mail(s) |
erika.kothe@uni-jena.de
|
| Organization name |
Friedrich-Schiller-University
|
| Department |
Microbial Communication, Institute of Microbiology
|
| Street address |
Neugasse 25
|
| City |
Jena |
| ZIP/Postal code |
07743 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11376 |
| Series (1) |
| GSE26401 |
Study of mating type genes and their roles in mating interactions of the basidiomycete Schizophyllum commune |
|
