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Items: 1 to 20 of 119

1.

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries.

Hafner M, Renwick N, Brown M, Mihailović A, Holoch D, Lin C, Pena JT, Nusbaum JD, Morozov P, Ludwig J, Ojo T, Luo S, Schroth G, Tuschl T.

RNA. 2011 Sep;17(9):1697-712. doi: 10.1261/rna.2799511. Epub 2011 Jul 20.

2.

Structural bias in T4 RNA ligase-mediated 3'-adapter ligation.

Zhuang F, Fuchs RT, Sun Z, Zheng Y, Robb GB.

Nucleic Acids Res. 2012 Apr;40(7):e54. doi: 10.1093/nar/gkr1263. Epub 2012 Jan 12.

3.

Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing.

Farazi TA, Brown M, Morozov P, Ten Hoeve JJ, Ben-Dov IZ, Hovestadt V, Hafner M, Renwick N, Mihailović A, Wessels LF, Tuschl T.

Methods. 2012 Oct;58(2):171-87. doi: 10.1016/j.ymeth.2012.07.020. Epub 2012 Jul 23.

4.

Identification of Taxus microRNAs and their targets with high-throughput sequencing and degradome analysis.

Hao DC, Yang L, Xiao PG, Liu M.

Physiol Plant. 2012 Dec;146(4):388-403. doi: 10.1111/j.1399-3054.2012.01668.x. Epub 2012 Jul 25.

PMID:
22708792
5.

Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing.

Hafner M, Renwick N, Farazi TA, Mihailović A, Pena JT, Tuschl T.

Methods. 2012 Oct;58(2):164-70. doi: 10.1016/j.ymeth.2012.07.030. Epub 2012 Aug 7.

6.
7.

Next-generation sequencing of miRNAs with Roche 454 GS-FLX technology: steps for a successful application.

Soares AR, Pereira PM, Santos MA.

Methods Mol Biol. 2012;822:189-204. doi: 10.1007/978-1-61779-427-8_13.

PMID:
22144200
8.

Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing.

Kawano M, Kawazu C, Lizio M, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y.

Biotechniques. 2010 Oct;49(4):751-5. doi: 10.2144/000113516.

9.

T4 RNA ligase 2 truncated active site mutants: improved tools for RNA analysis.

Viollet S, Fuchs RT, Munafo DB, Zhuang F, Robb GB.

BMC Biotechnol. 2011 Jul 1;11:72. doi: 10.1186/1472-6750-11-72.

10.

High-throughput multiplex sequencing of miRNA.

Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, C Christodoulou D, Seidman JG, Eisenberg E, M Church G.

Curr Protoc Hum Genet. 2012 Apr;Chapter 11:Unit 11.12.1-10. doi: 10.1002/0471142905.hg1112s73.

11.

Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I.

Lama L, Ryan K.

RNA. 2016 Jan;22(1):155-61. doi: 10.1261/rna.054999.115. Epub 2015 Nov 13.

PMID:
26567315
12.

Barcoding bias in high-throughput multiplex sequencing of miRNA.

Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, Church GM, Eisenberg E.

Genome Res. 2011 Sep;21(9):1506-11. doi: 10.1101/gr.121715.111. Epub 2011 Jul 12.

13.

Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing.

Kielpinski LJ, Boyd M, Sandelin A, Vinther J.

Methods Mol Biol. 2013;1038:213-31. doi: 10.1007/978-1-62703-514-9_13.

PMID:
23872978
14.

Sequencing bias: comparison of different protocols of microRNA library construction.

Tian G, Yin X, Luo H, Xu X, Bolund L, Zhang X, Gan SQ, Li N.

BMC Biotechnol. 2010 Sep 6;10:64. doi: 10.1186/1472-6750-10-64. Erratum in: BMC Biotechnol. 2011;11:48. Gan, Shang-Quang [added]; Li, Ning [added].

15.

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.

Jayaprakash AD, Jabado O, Brown BD, Sachidanandam R.

Nucleic Acids Res. 2011 Nov;39(21):e141. doi: 10.1093/nar/gkr693. Epub 2011 Sep 2.

16.

Methods for small RNA preparation for digital gene expression profiling by next-generation sequencing.

Linsen SE, Cuppen E.

Methods Mol Biol. 2012;822:205-17. doi: 10.1007/978-1-61779-427-8_14.

PMID:
22144201
17.

Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations.

Williams Z, Ben-Dov IZ, Elias R, Mihailovic A, Brown M, Rosenwaks Z, Tuschl T.

Proc Natl Acad Sci U S A. 2013 Mar 12;110(11):4255-60. doi: 10.1073/pnas.1214046110. Epub 2013 Feb 25.

18.

The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome.

Raabe CA, Hoe CH, Randau G, Brosius J, Tang TH, Rozhdestvensky TS.

RNA. 2011 Jul;17(7):1357-66. doi: 10.1261/rna.2682311. Epub 2011 May 24.

19.

Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing.

Peláez P, Trejo MS, Iñiguez LP, Estrada-Navarrete G, Covarrubias AA, Reyes JL, Sanchez F.

BMC Genomics. 2012 Mar 6;13:83. doi: 10.1186/1471-2164-13-83.

20.

Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing.

Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, Schaffer L, Deforce D, Salomon DR, Head SR, Ordoukhanian P.

PLoS One. 2011;6(10):e26969. doi: 10.1371/journal.pone.0026969. Epub 2011 Oct 28.

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