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| 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
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| 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
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| 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.
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| Contributor(s) |
Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G |
| Citation(s) |
19096707 |
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| Submission date |
Jun 16, 2008 |
| Last update date |
Jan 09, 2016 |
| Contact name |
Gavin Sherlock |
| E-mail(s) |
sherlock@genome.stanford.edu
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| Phone |
650 498 6012
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| Fax |
650 724 3701
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| URL |
http://genetics.stanford.edu/~sherlock/
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| Organization name |
Stanford University
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| Department |
Genetics
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| Street address |
300 Pasteur Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
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| Platforms (2) |
| GPL7249 |
[Sc03b_MF] Affymetrix GeneChip S. cerevisiae Tiling 1.0F Array |
| GPL7250 |
[Sc03b_MR] Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array |
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| Samples (8)
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| 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) |
| GSM298518 |
XRLP (xrn1 rrp6 lsm1 pat1) Mutant Salt Shock 30min rep1 (Watson strand; polyA RNA) |
| GSM298519 |
Isogenic WT Salt Shock 30min rep1 (Crick strand; Total RNA) |
| GSM298520 |
Isogenic WT Salt Shock 30min rep1 (Watson strand; Total RNA) |
| GSM298521 |
XRLP (xrn1 rrp6 lsm1 pat1) Mutant Salt Shock 30min rep1 (Crick strand; Total RNA) |
| GSM298522 |
XRLP (xrn1 rrp6 lsm1 pat1) Mutant Salt Shock 30min rep1 (Watson strand; Total RNA) |
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| This SubSeries is part of SuperSeries: |
| GSE11802 |
Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing |
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| Relations |
| BioProject |
PRJNA109081 |
| 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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