|
| Status |
Public on Nov 04, 2016 |
| Title |
FF_11_C_DD_C |
| Sample type |
RNA |
| |
|
| Source name |
FF1b MAT1-1 grown on cellulose in constant darkness
|
| Organism |
Trichoderma reesei |
| Characteristics |
strain: FF1b
mating type: MAT1-1
growth protocol: grown on cellulose in constant darkness
|
| Treatment protocol |
Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.
|
| Growth protocol |
Trichoderma reesei strains were grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1% microcrystalline cellulose as carbon source in constant darkness (DD) for 72 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Oligo-d(T) Primer.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
SAMPLE 6
one of two biological replicates
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
matrix_proteinIDs.txt (linked a supplementary file on the Series record) reports RMA signals for protein ID numbers which are similar in both Platform designs as they are based on homologues in the two T. reesei genomes on which the array is based.
|
| |
|
| Submission date |
Oct 24, 2016 |
| Last update date |
Nov 04, 2016 |
| Contact name |
Monika Schmoll |
| E-mail(s) |
monika.schmoll@univie.ac.at
|
| Organization name |
University of Vienna
|
| Department |
Centre of Microbiology and Environmental Systems Science
|
| Lab |
Division of Terrestrial Ecosystem Research
|
| Street address |
Djerassiplatz 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL10642 |
| Series (1) |
| GSE89103 |
Transcriptome analysis of T. reesei CBS999.97, backcrossed female fertile strains in QM6a genetic background and QM6a upon growth on cellulose |
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