Comment[ArrayExpressAccession]	E-GEOD-47840
MAGE-TAB Version	1.1								
Public Release Date	2013-09-01
Investigation Title	The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus								
Comment[Submitted Name]	The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series								
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl							
Person Last Name	Johansson								
Person First Name	Tomas								
Person Email	tomas.johansson@mbioekol.lu.se								
Person Affiliation	Lund University								
Person Phone	+46 46 222 45 49								
Person Address	Biology, Lund University, Sölvegatan 37, Lund, Sweden								
Person Roles	submitter								
Protocol Name	P-GSE47840-1	P-GSE47840-5	P-GSE47840-6	P-GSE47840-8	P-GSE47840-2	P-GSE47840-3	P-GSE47840-4	P-GSE47840-7	P-GSE47840-9
Protocol Description	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). ID_REF =  VALUE = RMA-normalized, averaged gene-level signal intensity (log2).	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 was performed using the NimbleGen Hybridization kit (#05 583 683 001) according to their Gene Expression v5.0 protocol (www.nimblegen.com).	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).	After N starvation there were 3 different treatments (each with 3 replicates) and involved the addition of either pollen, gliadin or BSA dissolved in MMN+glucose (inorganic N source excluded). Plates were then incubated for 7 days prior harvest.	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).	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).	Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 20% PMT.	Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 40% PMT.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol	array scanning protocol
Comment[SecondaryAccession]	GSE47840								
Comment[GEOReleaseDate]	2013-09-01								
Comment[ArrayExpressSubmissionDate]	2013-06-11								
Comment[GEOLastUpdateDate]	2013-09-03								
Comment[AEExperimentType]	transcription profiling by array								
SDRF File	E-GEOD-47840.sdrf.txt