Literature DB >> 25599667

Stranded Whole Transcriptome RNA-Seq for All RNA Types.

David F B Miller1, Pearlly X Yan2, Fang Fang1, Aaron Buechlein3, James B Ford3, Haixu Tang3, Tim H Huang4, Matthew E Burow5, Yunlong Liu6, Douglas B Rusch3, Kenneth P Nephew1.   

Abstract

Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to, miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non-coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA), and mRNA (messenger RNA). The size and nature of these types of RNA are irrelevant to the approach described here. Barcoded libraries for multiplexing on the Illumina platform are generated with this approach but it can be applied to other platforms with a few modifications.
Copyright © 2015 John Wiley & Sons, Inc.

Entities:  

Keywords:  RNA-Seq; duplex-specific nuclease; gene expression; transcriptome

Mesh:

Substances:

Year:  2015        PMID: 25599667      PMCID: PMC4337225          DOI: 10.1002/0471142905.hg1114s84

Source DB:  PubMed          Journal:  Curr Protoc Hum Genet        ISSN: 1934-8258


  7 in total

1.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

Authors:  K J Livak; T D Schmittgen
Journal:  Methods       Date:  2001-12       Impact factor: 3.608

2.  Predicting the sizes of large RNA molecules.

Authors:  Aron M Yoffe; Peter Prinsen; Ajaykumar Gopal; Charles M Knobler; William M Gelbart; Avinoam Ben-Shaul
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-09       Impact factor: 11.205

3.  The transcriptional landscape of the yeast genome defined by RNA sequencing.

Authors:  Ugrappa Nagalakshmi; Zhong Wang; Karl Waern; Chong Shou; Debasish Raha; Mark Gerstein; Michael Snyder
Journal:  Science       Date:  2008-05-01       Impact factor: 47.728

4.  Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome.

Authors:  Zhiyu Peng; Yanbing Cheng; Bertrand Chin-Ming Tan; Lin Kang; Zhijian Tian; Yuankun Zhu; Wenwei Zhang; Yu Liang; Xueda Hu; Xuemei Tan; Jing Guo; Zirui Dong; Yan Liang; Li Bao; Jun Wang
Journal:  Nat Biotechnol       Date:  2012-02-12       Impact factor: 54.908

5.  A new method for stranded whole transcriptome RNA-seq.

Authors:  David F B Miller; Pearlly S Yan; Aaron Buechlein; Benjamin A Rodriguez; Ayse S Yilmaz; Shokhi Goel; Hai Lin; Bridgette Collins-Burow; Lyndsay V Rhodes; Chris Braun; Sunila Pradeep; Rajesha Rupaimoole; Mehmet Dalkilic; Anil K Sood; Matthew E Burow; Haixu Tang; Tim H Huang; Yunlong Liu; Douglas B Rusch; Kenneth P Nephew
Journal:  Methods       Date:  2013-04-01       Impact factor: 3.608

6.  Selective depletion of rRNA enables whole transcriptome profiling of archival fixed tissue.

Authors:  John D Morlan; Kunbin Qu; Dominick V Sinicropi
Journal:  PLoS One       Date:  2012-08-10       Impact factor: 3.240

7.  Effects of the endocrine-disrupting chemical DDT on self-renewal and differentiation of human mesenchymal stem cells.

Authors:  Amy L Strong; Zhenzhen Shi; Michael J Strong; David F B Miller; Douglas B Rusch; Aaron M Buechlein; Erik K Flemington; John A McLachlan; Kenneth P Nephew; Matthew E Burow; Bruce A Bunnell
Journal:  Environ Health Perspect       Date:  2014-07-11       Impact factor: 9.031

  7 in total
  4 in total

1.  Differential gene expression in seasonal sympatry: mechanisms involved in diverging life histories.

Authors:  Adam M Fudickar; Mark P Peterson; Timothy J Greives; Jonathan W Atwell; Eli S Bridge; Ellen D Ketterson
Journal:  Biol Lett       Date:  2016-03       Impact factor: 3.703

Review 2.  RNA-Seq methods for transcriptome analysis.

Authors:  Radmila Hrdlickova; Masoud Toloue; Bin Tian
Journal:  Wiley Interdiscip Rev RNA       Date:  2016-05-19       Impact factor: 9.957

3.  NF-κB-HOTAIR axis links DNA damage response, chemoresistance and cellular senescence in ovarian cancer.

Authors:  A R Özeş; D F Miller; O N Özeş; F Fang; Y Liu; D Matei; T Huang; K P Nephew
Journal:  Oncogene       Date:  2016-04-04       Impact factor: 9.867

Review 4.  Long non-coding RNAs in cutaneous biology and proliferative skin diseases: Advances and perspectives.

Authors:  Lipeng Tang; Yongxin Liang; Hesong Xie; Xiaozhi Yang; Guangjuan Zheng
Journal:  Cell Prolif       Date:  2019-10-06       Impact factor: 6.831

  4 in total

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