E-MEXP-1257 - Transcription profiling of ectomycorrhizal fungus Paxillus involutus grown with different sources of nitrogen representing various degrees of complexity

Status
Released on 1 June 2008, last updated on 2 May 2014
Organism
Paxillus involutus
Samples (14)
Array (1)
Protocols (7)
Description
A microarray analysis to investigate transcriptional responses in the ectomycorrhizal fungus Paxillus involutus, after providing various sources of nitrogen. Five different sources of nitrogen representing various degrees of complexity were provided as patches in peat microcosms for fungal ingrowth: ammonium phosphate (APO), ammonium sulphate (ASU), glutamine (GLN), bovine serum albumin (BSA), and chitin (CHI). After fungal establishment of patches total RNA was isolated and used for global transcriptional analyses using cDNA microarrays. The entire design involved 9 slides (in the range DW2_01--DW2_13), 14 labelled extracts, and 3 biological replicates (R1-R3). The experiment was designed as a loop combining the 5 diffrent samples and including dye-swaps and biological replication. COMMENT: In our analysis of the raw dataset, 3 channels were removed due to poor signal quality: array 12707648b, Cy5 (635nm) channel (GLN R1 sample); array 12707650c, Cy5 (635nm) channel (APO R1 sample); array 12707651b, Cy5 (635nm) channel (APO R1 sample).
Experiment types
transcription profiling by array, co-expression, dye swap, growth condition, loop
Contact
Citation
Nutrient assimilation by the ectomycorrhizal fungus Paxillus involutus – Transcriptional responses in the extrametrical mycelium due to complexity of substrate. Tomas Johansson, Derek P. Wright, Antoine Le Quéré, Carl Troein, Carsten Pettersson, and Anders Tunlid.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MEXP-1257.idf.txt
Sample and data relationshipE-MEXP-1257.sdrf.txt
Raw data (1)E-MEXP-1257.raw.1.zip
Array designA-MEXP-853.adf.txt
R ExpressionSetE-MEXP-1257.eSet.r
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