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Series GSE40298 Query DataSets for GSE40298
Status Public on Nov 21, 2012
Title The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis
Organism Schizosaccharomyces pombe
Experiment type Expression profiling by high throughput sequencing
Summary Homeostatic control mechanisms are essentil to life. One such mechanism, the unfolded protein response (UPR) operates in all eukarytic cells to adjust protein folding capacity of the endoplasmic reticulum (ER) according to need. UPR induction in all eurkarytic cells to date involves Ire1 (kinase/endonuclease transmembrane protein) mediated a non-convential splicing of Hac1/XBP1 mRNA, encoding for a potent transcription factor. UPR induction causes a comprehensive transcriptional upregulation of the folding capacity in the ER. Here we studied the global transcriptional profile of the UPR in fission yeast. Fission yeast lacks a clear homolog of Hac1/XBP1. Instead Ire1 maintains ER homeostasis through two post-transciptional programs: selective mRNA decay and processing of Bip1 mRNA (encoding for a major HS70-familiy member in the ER) thereby stabilizing it.
Overall design S. pombe cells were grown in liquid medium (YE5S) to OD600=0.25. Cells were treated with or without 2 mM DTT (Dithiothreitol, impairs disulfid bond formation) for 60 min at 30℃. Total RNA was extracted from cells using hot phenol method. PolyA+ mRNA were enriched by two sequential rounds of oligo-dT (Invitrogen) selection. rRNA depletion was performed by depletion of ll RNA smaller than 200nt (mirVana miRNA Purification Kit (Ambion) followed by two rounds of subtractive hybridization using Ribominus EukaryoteKit for RNA-seq (Invitrogen). To sequence 2',3'-cyclic phosphate cleavage products tRNA ligase was used to selectively ligate an RNA linker to all 2',3'-cyclic phosphatesin total RNA. (described in Schutz et al., 2010). Two biological repeats were performed for the following samples with different conditions and yeast strains: poly A+ mRNA sample and mRNA enriched (ribosome depletion). On replicate was performed for RNA 3' end mapping carrying a 2',3'-cyclic phosphate: 1 replicate
Contributor(s) Kimmig P, Diaz M, Lang A, Zheng J, Williams C, Aragón T, Li H, Walter P
Citation(s) 23066505
Submission date Aug 22, 2012
Last update date May 15, 2019
Contact name Philipp Kimmig
Organization name University of California, San Francisco
Department Biochemistry and Biophysics
Lab Peter Walter lab
Street address Genentech Hall N316, 600 16th Street
City San Francisco
State/province CA
ZIP/Postal code 94158-2517
Country USA
Platforms (2)
GPL9453 Illumina Genome Analyzer II (Schizosaccharomyces pombe)
GPL13988 Illumina HiSeq 2000 (Schizosaccharomyces pombe)
Samples (15)
GSM991008 polyA+ enriched mRNA, WT -DTT Rep 1
GSM991009 polyA+ enriched mRNA, WT +DTT Rep 1
GSM991010 polyA+ enriched mRNA, Ire1Δ +DTT Rep 1
BioProject PRJNA173435
SRA SRP015005

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Supplementary file Size Download File type/resource
GSE40298_RAW.tar 100.7 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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