A comparison of microRNA sequencing reproducibility and noise reduction using mirVana and TRIzol isolation methods

International Journal of Computational Biology and Drug Design

Volumn 7, Issue 2-3, 2014, Pages 102-112

  Guo, Yan ^a   Bosompem, Amma ^b   Zhong, Xue ^a   Clark, Travis ^b   Shyr, Yu ^b   Kim, Annette S ^b  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VANDERBILT UNIVERSITY   (United States)

Author keywords

MicroRNA; MiRNA; MiRVana; Next generation sequencing; TRIzol

Indexed keywords

MICRORNA;

CONFERENCE PAPER; HUMAN; HUMAN CELL; LABORATORY DEVICE; NOISE REDUCTION; RNA ISOLATION; RNA SEQUENCE;

HUMANS; MICRORNAS; REAGENT KITS, DIAGNOSTIC; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, RNA;

EID: 84901945329     PISSN: 17560756     EISSN: 17560764     Source Type: Journal    
DOI: 10.1504/IJCBDD.2014.061642     Document Type: Conference Paper

References (19)

1. Asmann, Y.W., Klee, E.W., Thompson, E.A., Perez, E.A., Middha, S., Oberg, A.L., Therneau, T.M., Smith, D.I., Poland, G.A., Wieben, E.D. and Kocher, J.P. (2009) ' 3tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer' , BMC Genomics, Vol. 10, p.531.
2. Bartel, D.P. (2009) ' MicroRNAs: target recognition and regulatory functions' , Cell, Vol. 136, pp.215-233.
3. Bloom, J.S., Khan, Z., Kruglyak, L., Singh, M. and Caudy, A.A. (2009) ' Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays ', BMC Genomics, Vol. 10, p.221.
4. Chen, K. and Rajewsky, N. (2007) 'The evolution of gene regulation by transcription fact ors and microRNAs' , Nat. Rev. Genet., Vol. 8, pp.93-103. (Pubitemid 46122839)
5. Cloonan, N., Forrest, A.R., Kolle, G., Gardiner, B.B., Faulkner, G.J., Brown, M.K., Taylor, D.F., Steptoe, A.L., Wani, S., Bethel, G., Robertson, A.J., Perkins, A.C., Bruce, S.J., Lee, C.C., Ranade, S.S., Peckham, H.E., Manning, J.M., McKernan, K.J. and Grimmond, S.M. (2008) 'Stem cell transcriptome profiling via massive-scale mRNA sequencing ', Nat. Methods, Vol. 5, pp.613-619. (Pubitemid 351911866)
6. Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U. and Speed, T.P. (2003) ' Exploration, normalization, and summaries of high density oligonucleotide array probe level data ', Biostatistics, Vol. 4, pp.249-264.
7. Jiang Q.,Wang Y.,Hao Y.,Juan L.,Teng M.,Zhang X.,Li M.,Wang G.,Liu, Y. 2009 miR2Disease: a manually curated database for microRNA deregulation in human disease Nucleic Acids Research 37 D98-104.
8. Kim, Y.K., Yeo, J., Kim, B., Ha, M. and Kim, V.N. (2012) ' Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells' , Mol. Cell, Vol. 46, pp.893-895.
9. Kozomara, A. and Griffiths-Jones, S. (2011) ' miRBase: integrating microRNA annotation and deep-sequencing data' , Nucleic Acids Research, Vol. 39, pp.D152-157.
10. Kusenda, B., Mraz, M., Mayer, J. and Pospisilova, S. (2006) ' MicroRNA biogenesis, functionality and cancer relevance' , Biomed. Pap. Med. Fac. Univ. Palacky Olomouc Czech Repub., Vol. 150, pp.205-215.
11. Liu, F., Jenssen, T.K., Trimarchi, J., Punzo, C., Cepko, C.L., Ohno-Machado, L., Hovig, E. and Kuo, W.P. (2007) ' Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates ', BMC Genomics, Vol. 8, p.153.
12. Malone, J.H. and Oliver, B. (2011) 'Microarrays, deep sequencing and the true measure of the transcriptome ', BMC Biol., Vol. 9, p.34.
13. Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. and Gilad, Y. (2008) ' RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays ', Genome Res., Vol. 18, pp.1509-1517.
14. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold, B. (2008) ' Mapping and quantifying mammalian transcriptomes by RNA-Seq' , Nat. Methods, Vol. 5, pp.621-628. (Pubitemid 351911867)
15. Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlen, M. and Nielsen, J. (2012) ' A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae ', Nucleic Acids Res, Vol. 40, pp.10084-10097.
16. Sato, F., Tsuchiya, S., Terasawa, K. and Tsujimoto, G. (2009) ' Intra-platform repeatability and inter-platform comparability of microRNA microarray technology' , PLoS One, Vol. 4, p.e5540.
17. Su, Z., Li, Z., Chen, T., Li, Q.Z., Fang, H., Ding, D., Ge, W., Ning, B., Hong, H., Perkins, R.G., Tong, W. and Shi, L. (2011) 'Comparing next-ge neration sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys' , Chem. Res. Toxicol., Vol. 24, pp.1486-1493.
18. T Hoen, P.A., Ariyurek, Y., Thygesen, H.H., Vreugdenhil, E., Vossen, R.H., de Menezes, R.X., Boer, J.M., van Ommen, G.J. and den Dunnen, J.T. (2008) ' Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms ', Nucleic Acids Res., Vol. 36, p.e141.
19. Wilhelm, B.T., Marguerat, S., Goodhead, I. and Bahler, J. (2010) ' Defining transcribed regions using RNA-seq' , Nat. Protoc., Vol. 5, pp.255-266.