Comment[ArrayExpressAccession]	E-GEOD-28163
MAGE-TAB Version	1.1												
Public Release Date	2013-09-19
Investigation Title	Genotypic and Phenotypic Versatility of Aspergillus flavus during Maize Exploitation												
Comment[Submitted Name]	Genotypic and Phenotypic Versatility of Aspergillus flavus during Maize Exploitation
Experiment Description	Several are the inputs which are able to modulate mycotoxin synthesis. In particular, when a fungus receives an external stimulus reacts by activating, through a quite well-defined signal cascade, an evident switch in its lifestyle. This profound change is also due to the activation of global gene regulators and, in particular, of transcription factors able to switch on the mycotoxin gene clusters expression. Aflatoxins (AF) are harmful carcinogenic compounds produced mainly by Aspergillus flavus and A. parasiticus. AF are produced during the contamination of maize kernels into the field, even if their role in phyto-toxicity is not yet assessed. Nevertheless, AF biosynthesis is tightly regulated by host-derived signals. Recently, the nature of some of these signals have been elucidated. In particular, a role in susceptibility and resistance of maize to A. flavus contamination has been assigned to some plant oxylipins. These findings draw a scenario in which a complex interplay is under way between A. flavus and maize. For uncovering all the implications of this cross-talk we decide to follow a holistic approach. In particular, we designed experimental conditions aimed to mimic the different phases of A. flavus infection cycle on maize and then by performing a microarray analysis on the harvested mycelia. The microarray data set has been processed for performing the differential expression analysis of almost 14000 gene probes, the pathway analysis based on the gene ontology and inter pro annotations, the secondary metabolites cluster co-expression analysis and an identification of groups of co-expressed neighbor genes, possibly associated with production of secondary metabolites. Analysis of 12 microarrays monitoring gene expression of Aspergillus flavus over various growth conditions												
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	Uva	Reverberi	Punelli	Scala	Scarpari	Uva	Mentzen	Dolezal	Woloshuk	Pinzari	Fabbri	Fanelli	Payne
Person First Name	Paolo	M	M	V	M	P	W	A	C	F	A	C	G
Person Mid Initials							I	L			A		A
Person Email	paolo.uva@crs4.it												
Person Affiliation	CRS4												
Person Address	Bioinformatics, CRS4, Polaris, Pula, CA, Italy												
Person Roles	submitter												
Protocol Name	P-GSE28163-1	P-GSE28163-5	P-GSE28163-6	P-GSE28163-2	P-GSE28163-8	P-GSE28163-10	P-GSE28163-9	P-GSE28163-3	P-GSE28163-4	P-GSE28163-7			
Protocol Description	RMA background correction. Lowess normalization with JMP Genomics v3.0 ID_REF =  VALUE = Log2 RMA lowess normalized signal	Standard Affymetrix lab protocol	Standard Affymetrix lab protocol	Fifty ml of Czapek Dox Broth (CDB) (Difco) (which is low-conducive for aflatoxins) in was inoculated with the WT using 0.1 ml of conidial suspension for each flask; incubation was performed at 30°C up to 4 days. This growth condition is indicated as flask (i.e. the in vitro phase).	An amount (10g) of dead maize kernels (by autoclaving) were inoculated with 10000 conidia of NRRL 3357 in a sterile Petri plate and incubated at 30°C for 4d. This condition has been named as sapro (i.e. the saprophytic phase).	An amount of ~10000 conidia was used for infecting injured maize kernels directly onto maize ears in the field. The kernels were injured with the same needle used for inoculating the fungal conidia. This condition has been reported as vivo (i.e. the pathogenic phase).	0.1 ml of conidial suspension of A. flavus were incubated into 100-ml Erlenmeyer flasks containing CDB (50ml) and a dialysis membrane (cut off 7000 Da) in which 5 injured viable kernels were placed. This condition is subsequently reported as chemo phase (i.e. the chemotrophic phase). The dialysis membrane should allow the passage of small molecules from the injured kernels to the CDB medium.	The wild type (WT) used was Aspergillus flavus NRRL 3357, a producer of the aflatoxin B1. The isolates were incubated on Czapek Dox Agar (CDA) (Difco) for 7 days at 30°C, before use.	For total RNA extraction the Qiagen RNeasy kit RNA cleanup protocol was typically used, for most samples a phenol chloroform extraction protocol preceeded use of the RNeasy kit. For some samples phenol chloroform extractions and LiCl precipitation was used to purify RNA, this protocol is available from http://www.aspergillusflavus.org/protocols/.	Standard Affymetrix lab protocol			
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	sample treatment protocol	sample treatment protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol			
Publication Title	Genotypic and phenotypic versatility of Aspergillus flavus during maize exploitation.												
Publication Author List	Reverberi M, Punelli M, Scala V, Scarpari M, Uva P, Mentzen WI, Dolezal AL, Woloshuk C, Pinzari F, Fabbri AA, Fanelli C, Payne GA												
PubMed ID	23894339												
Publication DOI	10.1371/journal.pone.0068735												
Comment[SecondaryAccession]	GSE28163												
Comment[GEOReleaseDate]	2013-09-19												
Comment[ArrayExpressSubmissionDate]	2011-03-24												
Comment[GEOLastUpdateDate]	2013-09-21												
Comment[AEExperimentType]	transcription profiling by array												
SDRF File	E-GEOD-28163.sdrf.txt