Literature DB >> 19317658

High-throughput verification of transcriptional starting sites by Deep-RACE.

Signe Olivarius1, Charles Plessy, Piero Carninci.   

Abstract

We present a high-throughput method for investigating the transcriptional starting sites of genes of interest, which we named Deep-RACE (Deep-rapid amplification of cDNA ends). Taking advantage of the latest sequencing technology, it allows the parallel analysis of multiple genes and is free of time-consuming cloning steps. In comparison to the sequencing of RACE PCR products, our approach is more precise and more cost-effective even for batches as small as 17.

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Year:  2009        PMID： 19317658     DOI： 10.2144/000113066

Source DB:  PubMed          Journal:  Biotechniques        ISSN： 0736-6205            Impact factor:   1.993


  19 in total

1.  Activation of the Yeast UBI4 Polyubiquitin Gene by Zap1 Transcription Factor via an Intragenic Promoter Is Critical for Zinc-deficient Growth.

Authors:  Colin W MacDiarmid; Janet Taggart; Jeeyon Jeong; Kittikhun Kerdsomboon; David J Eide
Journal:  J Biol Chem       Date:  2016-07-18       Impact factor: 5.157

Review 2.  Annotating non-coding transcription using functional genomics strategies.

Authors:  Alistair R R Forrest; Rehab F Abdelhamid; Piero Carninci
Journal:  Brief Funct Genomic Proteomic       Date:  2009-11

3.  Polycomb preferentially targets stalled promoters of coding and noncoding transcripts.

Authors:  Daniel Enderle; Christian Beisel; Michael B Stadler; Moritz Gerstung; Prashanth Athri; Renato Paro
Journal:  Genome Res       Date:  2010-12-22       Impact factor: 9.043

4.  Discovery of ethanol-responsive small RNAs in Zymomonas mobilis.

Authors:  Seung Hee Cho; Roy Lei; Trey D Henninger; Lydia M Contreras
Journal:  Appl Environ Microbiol       Date:  2014-05-02       Impact factor: 4.792

5.  Transcriptional analysis of Deinococcus radiodurans reveals novel small RNAs that are differentially expressed under ionizing radiation.

Authors:  Chen-Hsun Tsai; Rick Liao; Brendan Chou; Lydia M Contreras
Journal:  Appl Environ Microbiol       Date:  2014-12-29       Impact factor: 4.792

6.  Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.

Authors:  Charles Plessy; Nicolas Bertin; Hazuki Takahashi; Roberto Simone; Md Salimullah; Timo Lassmann; Morana Vitezic; Jessica Severin; Signe Olivarius; Dejan Lazarevic; Nadine Hornig; Valerio Orlando; Ian Bell; Hui Gao; Jacqueline Dumais; Philipp Kapranov; Huaien Wang; Carrie A Davis; Thomas R Gingeras; Jun Kawai; Carsten O Daub; Yoshihide Hayashizaki; Stefano Gustincich; Piero Carninci
Journal:  Nat Methods       Date:  2010-06-13       Impact factor: 28.547

7.  Targeted rapid amplification of cDNA ends (T-RACE)--an improved RACE reaction through degradation of non-target sequences.

Authors:  Neil I Bower; Ian A Johnston
Journal:  Nucleic Acids Res       Date:  2010-09-15       Impact factor: 16.971

8.  The regulated retrotransposon transcriptome of mammalian cells.

Authors:  Geoffrey J Faulkner; Yasumasa Kimura; Carsten O Daub; Shivangi Wani; Charles Plessy; Katharine M Irvine; Kate Schroder; Nicole Cloonan; Anita L Steptoe; Timo Lassmann; Kazunori Waki; Nadine Hornig; Takahiro Arakawa; Hazuki Takahashi; Jun Kawai; Alistair R R Forrest; Harukazu Suzuki; Yoshihide Hayashizaki; David A Hume; Valerio Orlando; Sean M Grimmond; Piero Carninci
Journal:  Nat Genet       Date:  2009-04-19       Impact factor: 38.330

Review 9.  Emerging roles for long noncoding RNAs in skeletal biology and disease.

Authors:  Nguyen P T Huynh; Britta A Anderson; Farshid Guilak; Audrey McAlinden
Journal:  Connect Tissue Res       Date:  2016-06-02       Impact factor: 3.417

10.  Identification and characterization of small RNAs in Yersinia pestis.

Authors:  Arthur Beauregard; Eric A Smith; Brianna L Petrone; Navjot Singh; Christopher Karch; Kathleen A McDonough; Joseph T Wade
Journal:  RNA Biol       Date:  2013-01-16       Impact factor: 4.652
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