Transcriptomics

Dataset Information

0

Wt expression changes in deletion strain-conditioned media


ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae  

SUBMITTER: Frank C.P. Holstege  Eoghan O'Duibhir   Philip Lijnzaad    

PROVIDER: E-GEOD-54539 | ArrayExpress | 2014-05-14

SECONDARY ACCESSION(S): GSE54539PRJNA237312

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

Sorry, this publication's infomation has not been loaded in the Indexer, please go directly to PUBMED or Altmetric.

Similar Datasets

2014-05-14 | E-GEOD-54527 | ArrayExpress
2014-05-14 | E-GEOD-54528 | ArrayExpress
| GSE54528 | GEO
2014-08-27 | E-GEOD-55373 | ArrayExpress
2014-05-14 | E-MTAB-2218 | ArrayExpress
2005-01-01 | MODEL1011090000 | BioModels Database
| GSE54362 | GEO
2014-03-25 | BIOMD0000000527 | BioModels Database
2010-12-01 | E-GEOD-25736 | ArrayExpress
2016-03-25 | E-MTAB-4093 | ArrayExpress