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Title: wt expression changes in deletion strain-conditioned media      
dateReleased:
05-14-2014
description:
Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. This series shows the absence of media effects by growing wt strains in filtered medium in which slow-growing strains were grown previously. Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-54539
refinement:
raw
alternateIdentifiers:
54539
keywords:
functional genomics
dateModified:
06-03-2014
availability:
available
types:
gene expression
name:
Saccharomyces cerevisiae
ID:
A-GEOD-11232
name:
A-UMCU-Y16k-1.3
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-54539/E-GEOD-54539.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-54539/E-GEOD-54539.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=GSE54539
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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