|
| Status |
Public on Sep 01, 2013 |
| Title |
MMN+Glucose+NH4/36hrs (R2) |
| Sample type |
RNA |
| |
|
| Source name |
Treat MMN+Glucose+NH4/36hrs
|
| Organism |
Paxillus involutus |
| Characteristics |
strain: ATCC 200175
tissue: mycelium patch
|
| Treatment protocol |
After starvation the medium was replaced with BSA dissolved in MMN+glucose (inorganic N source excluded) and followed by incubation for 4 days. After this period of time there was either no addition or addition of 5mg of NH4Cl and continued incubation for either 14 or 36 hrs prior harvest (3 replicates for each).
|
| Growth protocol |
Paxillus involutus (Batsch) Fr. (ATCC 200175) was grown axenically in Petri dishes on a layer of glass beads immersed in medium. The fungus was first grown for 9 days on a Minimum Melin Norkrans (MMN)+glucose medium (in RT and in the dark). The cultures were then starved for nitrogen during 24 hrs, by replacing the medium by the same medium but excluding the nitrogen source (NH4Cl).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Harvest mycelium was immediately dropped into liquid nitrogen and homogenized in a mortar on dry ice. Total RNA was extracted using the Plant RNeasy Mini kit (www.qiagen.com) and concentrated using RNA MinElute kit (www.qiagen.com). RNA quality/integrity and concentration was assessed by analysis on a RNA 6000 Nano chip using the 2100 Bioanalyzer (Agilent). From total RNA, cDNA was produced using the SuperScript double-stranded cDNA Synthesis kit (Invitrogen, #11917-0xx) according to the NimbleGen Gene Expression v5.0 protocol (www.nimblegen.com).
|
| Label |
Cy3
|
| Label protocol |
Single-color labeling was performed using the Roche/NimbleGen One-Color DNA Labeling kit (# 05 223 55 001) following their Gene Expression v5.0 protocol (www.nimblegen.com).
|
| |
|
| Hybridization protocol |
Hybridization was performed using the NimbleGen Hybridization kit (#05 583 683 001) according to their Gene Expression v5.0 protocol (www.nimblegen.com).
|
| Scan protocol |
Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 40% PMT.
|
| Description |
Treat MMN+Glucose+NH4/36hrs; Replicate 2 (subarray A11)
|
| Data processing |
The bursted and gridded tif-files (.tif file) were directly subjected data extraction, background reduction and quantile normalization using the RMA (Robust Multi-Chip Average) algoritm as implemented by the NimbleScan software package, version 2.5.26 (Roche NimbleGen, Inc.)(www.nimblegen.com).
|
| |
|
| Submission date |
Jun 11, 2013 |
| Last update date |
Sep 01, 2013 |
| Contact name |
Tomas Johansson |
| E-mail(s) |
[email protected]
|
| Phone |
+46 46 222 45 49
|
| Organization name |
Lund University
|
| Department |
Biology
|
| Lab |
Microbial Ecology Group
|
| Street address |
Sölvegatan 37
|
| City |
Lund |
| ZIP/Postal code |
SE-223 62 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL14950 |
| Series (2) |
| GSE47839 |
Expression analysis from glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of nitrogen (+/-NH4) to substrate followed by incubation for different periods of time |
| GSE47840 |
The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus |
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