The mRNA Decay Resource:Protocols and Resources

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'''From the Jacobson lab'''<br>
'''From the Jacobson lab'''<br>
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He et al., 2008. Qualitative and quantitative assessment of the activity of the yeast nonsense-mediated mRNA decay pathway. Methods Enzymol. 449:127-47. [http://www.ncbi.nlm.nih.gov/pubmed/19215756|abstract] <br>
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He et al., 2008. Qualitative and quantitative assessment of the activity of the yeast nonsense-mediated mRNA decay pathway. Methods Enzymol. 449:127-47. [http://www.ncbi.nlm.nih.gov/pubmed/19215756] <br>
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<br>
'''From Fred Sherman'''<br>
'''From Fred Sherman'''<br>
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Sherman, 2002. Getting started with yeast.  Methods Enzymol. 350:3-41. [http://www.ncbi.nlm.nih.gov/pubmed?term=12073320|abstract] <br>
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Sherman, 2002. Getting started with yeast.  Methods Enzymol. 350:3-41. [http://www.ncbi.nlm.nih.gov/pubmed?term=12073320] <br>
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<br>
'''From Mike Culbertson'''<br>
'''From Mike Culbertson'''<br>
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Global measurement of mRNA half lives.  Guan et al., 2006. Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet. 2(11):e203. Epub 2006 Oct 18. [http://www.ncbi.nlm.nih.gov/pubmed?term=17166056|abstract] <br>
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Global measurement of mRNA half lives.  Guan et al., 2006. Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet. 2(11):e203. Epub 2006 Oct 18. [http://www.ncbi.nlm.nih.gov/pubmed?term=17166056] <br>
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==General RNA Protocols==
==General RNA Protocols==
Capped RNAs: <br>
Capped RNAs: <br>
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Bajak and Hagedorn, 2008. Efficient 5' cap-dependent RNA purification: use in identifying and studying subsets of RNA. Methods Mol Biol. 419:147-60. [http://www.ncbi.nlm.nih.gov/pubmed?term=18369981|abstract] <br>
+
Bajak and Hagedorn, 2008. Efficient 5' cap-dependent RNA purification: use in identifying and studying subsets of RNA. Methods Mol Biol. 419:147-60. [http://www.ncbi.nlm.nih.gov/pubmed?term=18369981] <br>
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Blewett et al., 2011. A quantitative assay for measuring mRNA decapping by splinted ligation reverse transcription polymerase chain reaction: qSL-RT-PCR. RNA 17(3):535-43. Epub 2011 Jan 10. [http://www.ncbi.nlm.nih.gov/pubmed/21220548|abstract] <br>
+
Blewett et al., 2011. A quantitative assay for measuring mRNA decapping by splinted ligation reverse transcription polymerase chain reaction: qSL-RT-PCR. RNA 17(3):535-43. Epub 2011 Jan 10. [http://www.ncbi.nlm.nih.gov/pubmed/21220548] <br>

Revision as of 16:10, 30 March 2011

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Protocols

Yeast protocols

From the Atkin lab
Total RNA extraction Support Protocol: Preparation of buffer saturated phenol
Measurement of Saccharomyces cerevisiae mRNA half lives
Measurement of Candida albicans mRNA half lives: Kebaara et al., 2006. Determination of mRNA half-lives in Candida albicans using thiolutin as a transcription inhibitor. Genome. 49(8):894-9. [1]
Yeast polyribosome preparation for RNA
Electrophoresis of RNA through gels containing formaldehyde
Northern transfer of RNA
Preparation of oligolabeled probes
Hybridization of RNA blots
Removal of oligolabeled probes from GeneScreen Plus membranes
Yeast polyribosome preparation - Proteins
Gel electrophoresis of proteins in denaturing conditions
Electrotransfer of proteins from polyacrylamide gels to membranes
Immunoblotting

From the Jacobson lab
He et al., 2008. Qualitative and quantitative assessment of the activity of the yeast nonsense-mediated mRNA decay pathway. Methods Enzymol. 449:127-47. [2]

From Fred Sherman
Sherman, 2002. Getting started with yeast. Methods Enzymol. 350:3-41. [3]

From Mike Culbertson
Global measurement of mRNA half lives. Guan et al., 2006. Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet. 2(11):e203. Epub 2006 Oct 18. [4]

General RNA Protocols

Capped RNAs:
Bajak and Hagedorn, 2008. Efficient 5' cap-dependent RNA purification: use in identifying and studying subsets of RNA. Methods Mol Biol. 419:147-60. [5]
Blewett et al., 2011. A quantitative assay for measuring mRNA decapping by splinted ligation reverse transcription polymerase chain reaction: qSL-RT-PCR. RNA 17(3):535-43. Epub 2011 Jan 10. [6]

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