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Series GSE11800 Query DataSets for GSE11800
Status Public on Dec 18, 2008
Title Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by genome tiling array
Summary A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions, how its transcriptional networks are controlled, and my provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well understood model eukaryote, we still do not have a full catalog and understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the aim of increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS) to identify and map the locations of unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells, revealing 540 currently unannotated, presumably low abundance or short-lived RNAs, of which 231 are previously unknown and unique to this study. It is likely that many of these represent cryptic unstable transcripts (CUTs) which are rapidly degraded and whose function(s) within the cell are still unclear, while others may represent novel functional transcripts. Of the 271 transcripts we identified in current intergenic regions, greater than 90 percent have lower conservation scores amongst closely related yeast species than 95 percent of the verified ORFs in S. cerevisiae; such regions of the genome have typically been less well studied, and by definition encode transcripts that distinguish S. cerevisiae from these closely related species.

Keywords: Saccharomyces cerevisiae, transcriptome, salt shock, xrn1, rrp6, lsm1, pat1, RNA degradation
Overall design Two samples, a wild-type reference and a mutant containing 4 deletions, were subjected to high salt shock, and total RNA was harvested. PolyA RNA was purified, and both polyA and total RNAs were hybridized to Forward and Reverse Affymetrix Tiling Microarrays. No replicates were done for any of the hybridizations.
Contributor(s) Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G
Citation(s) 19096707
Submission date Jun 16, 2008
Last update date Jan 09, 2016
Contact name Gavin Sherlock
Phone 650 498 6012
Fax 650 724 3701
Organization name Stanford University
Department Genetics
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platforms (2)
GPL7249 [Sc03b_MF] Affymetrix GeneChip S. cerevisiae Tiling 1.0F Array
GPL7250 [Sc03b_MR] Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array
Samples (8)
GSM298515 Isogenic WT Salt Shock 30min rep1 (Crick strand; polyA RNA)
GSM298516 Isogenic WT Salt Shock 30min rep1 (Watson strand; polyA RNA)
GSM298517 XRLP (xrn1 rrp6 lsm1 pat1) Mutant Salt Shock 30min rep1 (Crick strand; polyA RNA)
This SubSeries is part of SuperSeries:
GSE11802 Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing
BioProject PRJNA109081

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
GSE11800_RAW.tar 301.2 Mb (http)(custom) TAR (of BAR, CEL)
Processed data provided as supplementary file

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