Abstract
We summarize 12 experimental methods that have been developed for profiling gene expression by focusing on the 3′-end of poly(A+) mRNA, distilling both common and unique features. Of this family of methods, we provide detailed protocol for MAPS, a method we believe is the simplest and most cost-effective for profiling gene expression and quantifying alternative polyadenylation events by oligo-dT priming followed by random priming and deep sequencing. This method also enables library multiplexing by using a set of bar coding primers during PCR amplification. We also provide a general guideline for analysis of the data generated by MAPS by using the software package maps3end.
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Acknowledgments
We acknowledge early contribution of Kristi Fox-Walsh to this method. This work was supported by NIH grants (HG004659) to XDF.
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Zhou, Y., Li, HR., Huang, J., Jin, G., Fu, XD. (2014). Multiplex Analysis of PolyA-Linked Sequences (MAPS): An RNA-Seq Strategy to Profile Poly(A+) RNA. In: Rorbach, J., Bobrowicz, A. (eds) Polyadenylation. Methods in Molecular Biology, vol 1125. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-971-0_15
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DOI: https://doi.org/10.1007/978-1-62703-971-0_15
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Publisher Name: Humana Press, Totowa, NJ
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Online ISBN: 978-1-62703-971-0
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