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Series GSE91064 Query DataSets for GSE91064
Status Public on May 16, 2017
Title Study of ribosome dynamics after eIF5A depletion in budding yeast
Organism Saccharomyces cerevisiae
Experiment type Other
Summary eIF5A is an essential translation elongation factor present in all eukaryotes, and the only known protein to follow a post-translational modification called hypusination. Here, we performed a wide analysis of ribosome dynamics in S. cerevisiae eIF5A depleted cells using 5Pseq (Pelechano et al. 2015 PMID 26046441). This method allows the study of ribosome dynamics, by sequencing 5’ phosphorylated mRNA co-translational degradation intermediates. Since eIF5A is an essential protein in yeast, we used two eIF5A temperature-sensitive strains containing a single Pro83 to Ser mutation (tif51A-1) and double Cys39 to Tyr and Gly118 to Asp mutations (tif51A-3) in the highly expressed gene TIF51A (HYP2) that encodes eIF5A protein (Li et al. 2011 PMID: 24923804).
 
Overall design For our 5PSeq experiments we incubated the wild-type and the two eIF5A mutant cells at 37°C for 4 hours, conditions in which there is almost no drop in cell viability for both mutants but it can be observed an important reduction in eIF5A protein. We performed three independent 5PSeq experiments with each of the strains tif51A-1 (hyp2-1) and tif51A-3 (hyp2-3) and compared with two independent experiments with the isogenic wild-type BY4741 strain.
 
Contributor(s) Pelechano V, Alepuz P
Citation(s) 28549188
Submission date Dec 08, 2016
Last update date Mar 13, 2019
Contact name Vicent Pelechano
E-mail vicente.pelechano.garcia@ki.se
Organization name ScilifeLab - Karolinska Institutet
Department MTC
Street address Nobels väg 16
City Solna
ZIP/Postal code SE-17177
Country Sweden
 
Platforms (1)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (8)
GSM2420385 BY4741_rep2
GSM2420386 BY4741_rep3
GSM2420387 hyp2-1_rep1
Relations
BioProject PRJNA356767
SRA SRP094794

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
GSE91064_RAW.tar 19.9 Mb (http)(custom) TAR (of BEDGRAPH)
Raw data are available in SRA
Processed data provided as supplementary file

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