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Title: RNA sampling from a chemically diverse set of solid agar cultures of Aspergillus nidulans      
dateReleased:
04-04-2013
description:
In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 out of 16 known clusters and nearly accurate for the remaining three. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (super clusters), and validate this both with legacy data and experimentally by prediction and verification of a new supercluster consisting of the synthase AN1242 and the transferase AN11080. This normally requires extensive sets of combinatorial gene deletions. We have employed A. nidulansfor our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom. RNA was sampled from stabbed cultures on three different solid agar-based media (CYAs, YES, CYA) after 4, 8 or 10 days, resulting in a total of 8 samples.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-39993
refinement:
raw
alternateIdentifiers:
39993
keywords:
functional genomics
dateModified:
04-22-2013
availability:
available
types:
gene expression
name:
Emericella nidulans
ID:
A-GEOD-15913
name:
Agilent-031272 Aspergillus nidulans expression array V5
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-39993/E-GEOD-39993.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-39993/E-GEOD-39993.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39993
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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