Literature DB >> 21957044

Single-molecule direct RNA sequencing without cDNA synthesis.

Fatih Ozsolak1, Patrice M Milos.   

Abstract

Methods for in-depth genome-wide characterization of transcriptomes and quantification of transcript levels using various microarray and next-generation sequencing technologies have emerged as valuable tools for understanding cellular physiology and human disease biology and have begun to be utilized in various clinical diagnostic applications. Current methods, however, typically require RNA to be converted to complementary DNA prior to measurements. This step has been shown to introduce many biases and artifacts. In order to best characterize the 'true' transcriptome, the single-molecule direct RNA sequencing (DRS) technology was developed. This review focuses on the underlying principles behind the DRS, sample preparation steps, and the current and novel avenues of research and applications DRS offers.
Copyright © 2011 John Wiley & Sons, Ltd.

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Year:  2011        PMID: 21957044      PMCID: PMC3272359          DOI: 10.1002/wrna.84

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev RNA        ISSN: 1757-7004            Impact factor:   9.957


  37 in total

1.  Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models.

Authors:  E M Southern; U Maskos; J K Elder
Journal:  Genomics       Date:  1992-08       Impact factor: 5.736

Review 2.  Hybridization analyses of arrayed cDNA libraries.

Authors:  G G Lennon; H Lehrach
Journal:  Trends Genet       Date:  1991-10       Impact factor: 11.639

3.  Light-directed, spatially addressable parallel chemical synthesis.

Authors:  S P Fodor; J L Read; M C Pirrung; L Stryer; A T Lu; D Solas
Journal:  Science       Date:  1991-02-15       Impact factor: 47.728

4.  Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro.

Authors:  J D Roberts; B D Preston; L A Johnston; A Soni; L A Loeb; T A Kunkel
Journal:  Mol Cell Biol       Date:  1989-02       Impact factor: 4.272

5.  DNA-directed DNA polymerase activity in oncogenic RNA viruses.

Authors:  S Spiegelman; A Burny; M R Das; J Keydar; J Schlom; M Travnicek; K Watson
Journal:  Nature       Date:  1970-09-05       Impact factor: 49.962

6.  Second-strand cDNA synthesis: mRNA fragments as primers.

Authors:  U Gubler
Journal:  Methods Enzymol       Date:  1987       Impact factor: 1.600

7.  A high-resolution map of transcription in the yeast genome.

Authors:  Lior David; Wolfgang Huber; Marina Granovskaia; Joern Toedling; Curtis J Palm; Lee Bofkin; Ted Jones; Ronald W Davis; Lars M Steinmetz
Journal:  Proc Natl Acad Sci U S A       Date:  2006-03-28       Impact factor: 11.205

8.  Fidelity of enzymatic ligation for DNA computing.

Authors:  D Faulhammer; R J Lipton; L F Landweber
Journal:  J Comput Biol       Date:  2000       Impact factor: 1.479

9.  Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites.

Authors:  Joel H Graber; Gregory D McAllister; Temple F Smith
Journal:  Nucleic Acids Res       Date:  2002-04-15       Impact factor: 16.971

10.  Mapping adenines, guanines, and pyrimidines in RNA.

Authors:  H Donis-Keller; A M Maxam; W Gilbert
Journal:  Nucleic Acids Res       Date:  1977-08       Impact factor: 16.971

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  23 in total

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3.  Transcriptional control and transcriptomic analysis of lipid metabolism in skin barrier formation and atopic dermatitis (AD).

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Review 4.  Promising new assays and technologies for the diagnosis and management of infectious diseases.

Authors:  S F Mitsuma; M K Mansour; J P Dekker; J Kim; M Z Rahman; A Tweed-Kent; P Schuetz
Journal:  Clin Infect Dis       Date:  2012-12-07       Impact factor: 9.079

Review 5.  How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape?

Authors:  Islam Hamim; Ken-Taro Sekine; Ken Komatsu
Journal:  Plant Mol Biol       Date:  2022-08-13       Impact factor: 4.335

Review 6.  Genomic sequencing in cancer.

Authors:  Musaffe Tuna; Christopher I Amos
Journal:  Cancer Lett       Date:  2012-11-23       Impact factor: 8.679

7.  Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection.

Authors:  Zhao Zhang; William E Theurkauf; Zhiping Weng; Phillip D Zamore
Journal:  Silence       Date:  2012-12-28

Review 8.  Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers.

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Journal:  J Cancer       Date:  2015-05-01       Impact factor: 4.207

9.  Cell type-specific gene expression profiling in brain tissue: comparison between TRAP, LCM and RNA-seq.

Authors:  TaeHyun Kim; Chae-Seok Lim; Bong-Kiun Kaang
Journal:  BMB Rep       Date:  2015-07       Impact factor: 4.778

10.  Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

Authors:  Nicholas J Schurch; Christian Cole; Alexander Sherstnev; Junfang Song; Céline Duc; Kate G Storey; W H Irwin McLean; Sara J Brown; Gordon G Simpson; Geoffrey J Barton
Journal:  PLoS One       Date:  2014-04-10       Impact factor: 3.240

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