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Series GSE13653 Query DataSets for GSE13653
Status Public on May 12, 2009
Title Affinity purification of ribosomes and associated RNAs from stress-treated cells
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary In this study, we systematically identified ribosome associated RNAs. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a, expressed under control of its native promoter, was affinity purified from whole cell extracts of cultures grown to mid-log phase. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. To analyze how changes in steady-state mRNA levels (= transcriptome) are related to changes of respective messages in the translatome, total RNA and ribosome associated RNA from stress-treated and untreated cells were analyzed with yeast cDNA microarrays. To achieve this, fluorescently labeled (Cy5) cDNA was prepared from total RNA isolated from yeast cell extracts and from affinity-purified ribosomes, and each sample was mixed with differentially labeled (Cy3) cDNA prepared from a common reference RNA pool, and competitively hybridized on yeast cDNA microarrays. We performed five independent experiments with untreated cells grown in minimal medium (t=0 reference) and three or more independent biological replicates of treated cells. Altogether, we sampled the cell's response to five different "stress treatments" that were applied for relatively short periods of time (10 or 20 minutes) to avoid secondary effects triggered by transcriptional adaption.
A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment
Time: Duration of the treatment
Growth Condition: Type of treatment

Overall design stimulus_or_stress_design
Contributor(s) Halbeisen R
Citation(s) 19419242
Submission date Nov 18, 2008
Last update date Jan 18, 2013
Contact name Andre Gerber
Phone +41 44 6337378
Fax +41 44 6337364
Organization name Swiss Federal Institute of Technology
Department Institute of Pharmaceutical Science
Street address Wolfgang Pauli Str. 10, HCI H396
City ETH Hoenggerberg, Zuerich
ZIP/Postal code ZH
Country Switzerland
Platforms (1)
GPL7662 Saccharomyces cerevisiae 9.2K Print_1137
Samples (52)
GSM343518 RPL16a-ZZ total vs reference (5)
GSM343519 RPL16a-ZZ total vs reference (3)
GSM343520 AAs starvation RPL16a-ZZ IP poly vs reference (3)
This SubSeries is part of SuperSeries:
GSE13682 Affinity purification of ribosomes and associated RNAs from stress-treated cells using tagged Rpl16a and Rpl16b
BioProject PRJNA113893

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE13653_RAW.tar 660.0 Kb (http)(custom) TAR
Processed data included within Sample table

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