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New PDF release: Cap-Analysis Gene Expression (CAGE): The Science of Decoding

By Piero Carninci

ISBN-10: 9814241342

ISBN-13: 9789814241342

A advisor for clients of recent applied sciences, this quantity contains properly confirmed protocols, permitting readers to arrange their samples for experiments. also, it presents a advisor for the bioinformatics instruments which are to be had for the research of the acquired tags, together with the layout of the software program, the assets and internet info the place they are often downloaded. ultimately, the booklet offers examples of the appliance of those applied sciences to spot promoters, annotate genomes, establish new RNAs and reconstruct versions of transcriptional keep an eye on. even though examples usually regard mammalians, the dialogue expands to different teams of eukaryotes, the place those methods are complementing genome sequencing.

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Additional resources for Cap-Analysis Gene Expression (CAGE): The Science of Decoding Gene Transcription

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USA. 100, 1577–1581 (2003). [13] R. Kodzius et al. CAGE: Cap analysis of gene expression. Nat. Methods. 3, 211–222 (2006). [14] P. Carninci et al. Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA. Proc. Natl. Acad. Sci. USA 95, 520–524 (1998). 19 September 4, 2009 20 10:22 RPS: Pan Stanford Publishing Book - 6in x 9in References [15] P. Carninci, T. Shiraki, Y. Mizuno, M. Muramatsu & Y. Hayashizaki, Extra-long first-strand cDNA synthesis.

1 × TE buffer and chloroform. Total volume should be around 650 µL. (6) Divide the sample into 2 tubes and add 17 µL of 5 M NaCl and 325 µL of ethanol. 1 × TE. 5 µL of sample solution by picogreen (Invitrogen). 10 STAGE 9: CONCATENATION Sanger sequencing has been typically used to read CAGE libraries,1 but due to the cost, this is not used any more. In our experience, at least 500 ng of tags is necessary for the concatenation in GS20/GSFLX systems (454 Life Sciences). The concatenation takes place by addition during the ligation steps with the “454” linkers; these can ligate only at one of their sides and act as “ligase terminators”.

Mapping and quantifying mammalian transcriptomes by RNASeq. Nat. Methods 5, 621–8 (2008). [24] P. G. Engstrom et al. Complex Loci in human and mouse genomes. PLoS Genet. 2, e47 (2006). [25] E. Birney et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007). [26] H. Kawaji et al. Dynamic usage of transcription start sites within core promoters. Genome Biol. 7, R118 (2006). 2 Based on the same protocol, CAGE will work with the Illumina GA or GA2 or the SOLiD sequencing instruments, provided that the user changes the the linkers and adaptors to fit the needs of other platforms.

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Cap-Analysis Gene Expression (CAGE): The Science of Decoding Gene Transcription by Piero Carninci

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