The mRNA Decay Resource:Protocols and Resources

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==Yeast protocols==
==Yeast protocols==
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=From the Atkin lab= <br>
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'''From the Kebaara, Baker and Atkin labs''' <br>
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[[Media:RNAextrc.pdf|Total RNA extraction]] Support Protocol: [Media:rnapheno.pdf|Preparation of buffer saturated phenol] <br>
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Kebaara, B. W., K. E. Baker, K. D. Patefield and A. L. Atkin, 2012.  Analysis of Nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Current Protocols in Cell Biology Chapter 27:Unit27.3. [http://www.ncbi.nlm.nih.gov/pubmed/22422476] <br><br>
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[Media:mrnahalf.pdf|Measurement of mRNA half lives] <br>
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[Media:PlyriRNA.pdf|Yeast polyribosome preparation for RNA] <br>
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'''From the Atkin lab'''<br>
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[Media:RNAgels.pdf|Electrophoresis of RNA through gels containing formaldehyde] <br>
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Atkin, A. L., 2011. Yeast bioinformatics and strain engineering resources.  Methods in Molecular Biology, vol. 765, Strain Engineering: Methods and Protocols, Ed. J. A. Williams, Humana Press Inc., Totowa, NJ. pp 173-187. [http://www.ncbi.nlm.nih.gov/pubmed/21815093] <br>
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[Media:NorthRNA.pdf|Northern transfer of RNA] <br>
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Kebaara et al., 2006.  Determination of mRNA half-lives in ''Candida albicans'' using thiolutin as a transcription inhibitor. Genome. 49(8):894-9. [http://www.ncbi.nlm.nih.gov/pubmed?term=17036064] <br>
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[Media:dnaprobe.pdf|Preparation of oligolabeled probes] <br>
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Atkin, A. L., 1999.  Preparation of yeast cells for confocal microscopy.  Methods in Molecular Biology, vol. 122:  Confocal Microscopy Methods and Protocols Ed. S. Paddock, Humana Press Inc., Totowa, NJ. pp. 131-139. [http://www.ncbi.nlm.nih.gov/pubmed/10231788] <br>
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[Media:hybrdRNA.pdf|Hybridization of RNA blots] <br>
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[[Media:PlyriRNA.pdf|Yeast polyribosome preparation for RNA]] <br>
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[Media:Remov32P.pdf|Removal of oligolabeled probes for GeneScreen <I>Plus</I> membranes] <br>
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[[Media:plyriprot.pdf|Yeast polyribosome preparation for Proteins]] <br>
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[Media:plyriprot.pdf|Yeast polyribosome preparation - Proteins] <br>
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[[Media:protgel.pdf|Gel electrophoresis of proteins in denaturing conditions]] <br>
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[Media:protgel.pdf|Gel electrophoresis of proteins in denaturing conditions] <br>
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[[Media:protran.pdf|Electrotransfer of proteins from polyacrylamide gels to membranes]] <br>
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[Media:protran.pdf|Electrotransfer of proteins from polyacrylamide gels to membranes] <br>
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[[Media:imblot.pdf|Immunoblotting]] <br>
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[Media:imblot.pdf|Immunoblotting] <br>
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<br>
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'''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] <br>
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<br>
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'''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] <br>
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<br>
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'''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] <br>
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<br>
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==General RNA Protocols==
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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] <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] <br>

Current revision

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Protocols

Yeast protocols

From the Kebaara, Baker and Atkin labs
Kebaara, B. W., K. E. Baker, K. D. Patefield and A. L. Atkin, 2012. Analysis of Nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Current Protocols in Cell Biology Chapter 27:Unit27.3. [1]

From the Atkin lab
Atkin, A. L., 2011. Yeast bioinformatics and strain engineering resources. Methods in Molecular Biology, vol. 765, Strain Engineering: Methods and Protocols, Ed. J. A. Williams, Humana Press Inc., Totowa, NJ. pp 173-187. [2]
Kebaara et al., 2006. Determination of mRNA half-lives in Candida albicans using thiolutin as a transcription inhibitor. Genome. 49(8):894-9. [3]
Atkin, A. L., 1999. Preparation of yeast cells for confocal microscopy. Methods in Molecular Biology, vol. 122: Confocal Microscopy Methods and Protocols Ed. S. Paddock, Humana Press Inc., Totowa, NJ. pp. 131-139. [4]
Yeast polyribosome preparation for RNA
Yeast polyribosome preparation for 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. [5]

From Fred Sherman
Sherman, 2002. Getting started with yeast. Methods Enzymol. 350:3-41. [6]

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. [7]

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. [8]
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. [9]

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