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| Status |
Public on Jan 06, 2016 |
| Title |
Comparison of alternative decapping enzymes to map transcription start sites genome-wide |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The production of Tobacco Acid Pyrophosphatase (TAP), an enzyme commonly used for the removal of the 5’cap of eukaryotic mRNAs, has been recently discontinued. Here we performed a comparison of current alternatives for the mapping of 5’cap mRNAs and the associated transcription start sites in Sacharomyces cerevisiae. Specifically we compared TAP with Cap-clip and a Decapping Pyrophosphohydrolase. Our results suggest that Cap-clip is a good alternative for TAP.
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| Overall design |
We used two biological replicates of S. cerevisiae that was grown to exponential phase (OD600 ~1) in rich media (YPAD). Samples where processed until the dephosphorylation step (CIP treatment). After that each sample was split in 4 aliquots: TAP treatment, Cap-Clip treatment, Decapping Pyrophosphohydrolase treatment or no treatment (negative control). From that step all samples are processed in parallel.
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| Contributor(s) |
Pelechano V, Wei W, Steinmetz LM |
| Citation(s) |
26046441 |
| Submission date |
Oct 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wu Wei |
| E-mail(s) |
wuwei@embl.de
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| Organization name |
EMBL Heidelberg
|
| Department |
Genome Biology Unit
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| Lab |
Steinmetz Lab
|
| Street address |
EMBL Heidelberg,Meyerhofstraße 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69117 |
| Country |
Germany |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA298055 |
| SRA |
SRP064577 |
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