|
| Status |
Public on May 19, 2015 |
| Title |
Ppl_17_A_3_rep_1 |
| Sample type |
RNA |
| |
|
| Source name |
P. placenta on subsatrate A after 30 days
|
| Organism |
Postia placenta |
| Characteristics |
substrate: A: high lignin, low glucose
incubation time(days): 30
tissue: Mycelium
strain: MAD-698-R
|
| Treatment protocol |
Poplar wood stems were cut into 0.5 mm wafers on a microtome, sterilized for 20 min at 121°C, dried at 50°C overnight, and cooled to room temperature. The specimens were then inoculated in Petri dishes with actively growing mycelia. Approximately 5 g of wood wafers were placed in each Petri dish (exact weights were recorded), sealed and incubated at 22°C and 70 ± 5% relative humidity for 10, 20 or 30 days (time points: 10, 20 and 30, respectively). Following incubation, the wafers were removed from the Petri dishes, immediately snap-frozen in liquid nitrogen and stored at -80°C for later use. For substrates “A” and “B”, three(1) replicates were used for each substrate/fungus and incubation period combination. For substrate “C” only 2 biological replicates were employed. (1)One of the tree replicates of substrate B after 10 days failes, therfore only 2 replicates were used .
|
| Growth protocol |
P. placenta was cultured on malt extract agar (MEA) (Oxoid, UK) for 10 days prior to inoculation with wood wafers.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen wood wafers with fungal mycelia were ground to a fine powder with liquid nitrogen in an acid washed, pre-chilled mortar and pestle. Total fungal RNA was purified as previously described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610).
|
| Label |
Cy3
|
| Label protocol |
Labelling was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) following NimbleGen standard operating protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) following NimbleGen standard operating protocol.
|
| Scan protocol |
Scanningn was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) using Axon4000B Scanner( Molecular Dynamics)
|
| Description |
This sample is of P. placenta incubated on substrate A for 30 days. It is the first of three biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization , and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
May 18, 2015 |
| Last update date |
May 19, 2015 |
| Contact name |
Shawn Mansfield |
| E-mail(s) |
shawn.mansfield@ubc.ca
|
| Organization name |
University of British Columbia
|
| Department |
Department of Wood Science
|
| Street address |
2424 Main Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL7187 |
| Series (2) |
| GSE69004 |
Postia placenta gene expression on different substrates |
| GSE69012 |
ene expression patterns of wood decay fungi Postia placenta and Phanerochaete chrysosporium are influenced by wood substrate composition during degradation |
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