Potential pitfalls in microRNA profiling

Wiley Interdisciplinary Reviews: RNA

Volumn 3, Issue 5, 2012, Pages 601-616

  Chugh, Pauline ^a   Dittmer, Dirk P ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

BIOINFORMATICS; DISEASE MARKER; HUMAN; MICROARRAY ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REPRODUCIBILITY; REVIEW; RNA ANALYSIS; RNA EDITING; RNA PROCESSING; RNA SEQUENCE; SAMPLING; SEQUENCE ANALYSIS;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; NEOPLASMS; RNA PROCESSING, POST-TRANSCRIPTIONAL; SPECIMEN HANDLING; VIRUS DISEASES;

EID: 84867619796     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1120     Document Type: Review

References (111)

1. Sun G, Li H, Rossi JJ. Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3′ UTR. Nucleic Acids Res 2010, 38:239-252.
2. Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol 2005, 3:e85.
3. Didiano D, Hobert O. Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol 2006, 13:849-851.
4. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, 34:D140-D144.
5. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-D158.
6. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157.
7. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res 2004, 32:D109-D111.
8. Gottwein E, Cai X, Cullen BR. A novel assay for viral microRNA function identifies a single nucleotide polymorphism that affects Drosha processing. J Virol 2006, 80:5321-5326.
9. Marshall V, Martro E, Labo N, Ray A, Wang D, Mbisa G, Bagni RK, Volfovsky N, Casabona J, Whitby D. Kaposi sarcoma (KS)-associated herpesvirus microRNA sequence analysis and KS risk in a European AIDS-KS case control study. J Infect Dis 2010, 202:1126-1135.
10. Marshall V, Parks T, Bagni R, Wang CD, Samols MA, Hu J, Wyvil KM, Aleman K, Little RF, Yarchoan R, et al. Conservation of virally encoded microRNAs in Kaposi sarcoma-associated herpesvirus in primary effusion lymphoma cell lines and in patients with Kaposi sarcoma or multicentric Castleman disease. J Infect Dis 2007, 195:645-659.
11. Lei X, Bai Z, Ye F, Xie J, Kim CG, Huang Y, Gao SJ. Regulation of NF-κB inhibitor IκBα and viral replication by a KSHV microRNA. Nat Cell Biol 2010, 12:193-199.
12. O'Hara AJ, Chugh P, Wang L, Netto EM, Luz E, Harrington WJ, Dezube BJ, Damania B, Dittmer DP. Pre-micro RNA signatures delineate stages of endothelial cell transformation in Kaposi sarcoma. PLoS Pathog 2009, 5:e1000389.
13. Hansen A, Henderson S, Lagos D, Nikitenko L, Coulter E, Roberts S, Gratrix F, Plaisance K, Renne R, Bower M, et al. KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming. Genes Dev 2010, 24:195-205.
14. Lu F, Stedman W, Yousef M, Renne R, Lieberman PM. Epigenetic regulation of Kaposi's sarcoma-associated herpesvirus latency by virus-encoded microRNAs that target Rta and the cellular Rbl2-DNMT pathway. J Virol 2010, 84:2697-2706.
15. Qin Z, Freitas E, Sullivan R, Mohan S, Baceliere R, Branch D, Romano M, Kearney P, Oates J, Plaisance K, et al. Upregulation of xCT by KSHV-encoded microRNAs facilitates KSHV dissemination and persistence in an environment of oxidative stress. PLoS Pathog 2010, 6:e1000742.
16. Boss IW, Renne R. Viral miRNAs and immune evasion. Biochim Biophys Acta 2011, 1809:708-714.
17. Chandriani S, Xu Y, Ganem D. The lytic transcriptome of Kaposi's sarcoma-associated herpesvirus reveals extensive transcription of noncoding regions, including regions antisense to important genes. J Virol 2010, 84:7934-7942.
18. Lin YT, Kincaid RP, Arasappan D, Dowd SE, Hunicke-Smith SP, Sullivan CS. Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs. RNA 2010, 16:1540-1558.
19. Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien M, et al. Identification of microRNAs of the herpesvirus family. Nat Methods 2005, 2:269-276.
20. Rachamadugu R, Lee JY, Wooming A, Kong BW. Identification and expression analysis of infectious laryngotracheitis virus encoding microRNAs. Virus Genes 2009, 39:301-308.
21. Riley KJ, Rabinowitz GS, Steitz JA. Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression. J Virol 2010, 84:5148-5157.
22. Xu H, Yao Y, Zhao Y, Smith LP, Baigent SJ, Nair V. Analysis of the expression profiles of Marek's disease virus-encoded microRNAs by real-time quantitative PCR. J Virol Methods 2008, 149:201-208.
23. Zhu JY, Strehle M, Frohn A, Kremmer E, Hofig KP, Meister G, Adler H. Identification and analysis of expression of novel microRNAs of murine γ herpesvirus 68. J Virol 2010, 84:10266-10275.
24. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 2005, 436:740-744.
25. Cui L, Guo X, Qi Y, Qi X, Ge Y, Shi Z, Wu T, Shan J, Shan Y, Zhu Z, et al. Identification of microRNAs involved in the host response to enterovirus 71 infection by a deep sequencing approach. J Biomed Biotechnol 2010, 2010:425939.
26. Kong BW. Identification of virus encoding microRNAs using 454 FLX sequencing platform. Methods Mol Biol 2011, 733:81-91.
27. Li LM, Hu ZB, Zhou ZX, Chen X, Liu FY, Zhang JF, Shen HB, Zhang CY, Zen K. Serum microRNA profiles serve as novel biomarkers for HBV infection and diagnosis of HBV-positive hepatocarcinoma. Cancer Res 2010, 70:9798-9807.
28. Li SC, Shiau CK, Lin WC. Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic Acids Res 2008, 36:D184-D189.
29. Qi Y, Tu J, Cui L, Guo X, Shi Z, Li S, Shi W, Shan Y, Ge Y, Shan J, et al. High-throughput sequencing of microRNAs in adenovirus type 3 infected human laryngeal epithelial cells. J Biomed Biotechnol 2010, 2010:915980.
30. Sullivan CS, Sung CK, Pack CD, Grundhoff A, Lukacher AE, Benjamin TL, Ganem D. Murine Polyomavirus encodes a microRNA that cleaves early RNA transcripts but is not essential for experimental infection. Virology 2009, 387:157-167.
31. Umbach JL, Cullen BR. In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J Virol 2010, 84:695-703.
32. Varnholt H, Drebber U, Schulze F, Wedemeyer I, Schirmacher P, Dienes HP, Odenthal M. MicroRNA gene expression profile of hepatitis C virus-associated hepatocellular carcinoma. Hepatology 2008, 47:1223-1232.
33. Wang Y, Brahmakshatriya V, Zhu H, Lupiani B, Reddy SM, Yoon BJ, Gunaratne PH, Kim JH, Chen R, Wang J. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genom 2009, 10:512.
34. Witwer KW, Sarbanes SL, Liu J, Clements JE. A plasma microRNA signature of acute lentiviral infection: biomarkers of central nervous system disease. AIDS 2011, 25:2057-2067.
35. Wong AM, Kong KL, Tsang JW, Kwong DL, Guan XY. Profiling of Epstein-Barr virus-encoded microRNAs in nasopharyngeal carcinoma reveals potential biomarkers and oncomirs. Cancer 2011, 118:698-710.
36. Zhou J, Yu L, Gao X, Hu J, Wang J, Dai Z, Wang JF, Zhang Z, Lu S, Huang X, et al. Plasma microRNA panel to diagnose hepatitis B virus-related hepatocellular carcinoma. J Clin Oncol 2011, 29:4781-4788.
37. Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, Gibson DJ, Mitchell PS, Bennett CJ, Pogosova-Agadjanyan EL, Stirewalt DL, et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A 2011, 108:5003-5008.
38. Chang J, Nicolas E, Marks D, Sander C, Lerro A, Buendia MA, Xu C, Mason WS, Moloshok T, Bort R, et al. miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol 2004, 1:106-113.
39. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu AL, et al. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res 2008, 18:1787-1797.
40. O'Hara AJ, Vahrson W, Dittmer DP. Gene alteration and precursor and mature microRNA transcription changes contribute to the miRNA signature of primary effusion lymphoma. Blood 2008, 111:2347-2353.
41. Wang LG, Gu J. Serum microRNA-29a is a promising novel marker for early detection of colorectal liver metastasis. Cancer Epidemiol 2011, 36:e61-e67.
42. Wei J, Gao W, Zhu CJ, Liu YQ, Mei Z, Cheng T, Shu YQ. Identification of plasma microRNA-21 as a biomarker for early detection and chemosensitivity of non-small cell lung cancer. Chin J Cancer 2011, 30:407-414.
43. Zhang Y, Jia Y, Zheng R, Guo Y, Wang Y, Guo H, Fei M, Sun S. Plasma microRNA-122 as a biomarker for viral-, alcohol-, and chemical-related hepatic diseases. Clin Chem 2010, 56:1830-1838.
44. Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell 17 2003, 115:209-216.
45. Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD. A protein sensor for siRNA asymmetry. Science 2004, 306:1377-1380.
46. Maniataki E, Mourelatos Z. A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. Genes Dev 2005, 19:2979-2990.
47. Hammond SM, Bernstein E, Beach D, Hannon GJ. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2000, 404:293-296.
48. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115:199-208.
49. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005, 33:e179.
50. Kauppinen S, Vester B, Wengel J. Locked nucleic acid: high-affinity targeting of complementary RNA for RNomics. Handb Exp Pharmacol 2006, 173:405-422.
51. Sato F, Tsuchiya S, Terasawa K, Tsujimoto G. Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One 2009, 4:e5540.
52. Jang JS, Simon VA, Feddersen RM, Rakhshan F, Schultz DA, Zschunke MA, Lingle WL, Kolbert CP, Jen J. Quantitative miRNA expression analysis using fluidigm microfluidics dynamic arrays. BMC Genom 2011, 12:144.
53. Moltzahn F, Olshen AB, Baehner L, Peek A, Fong L, Stoppler H, Simko J, Hilton JF, Carroll P, Blelloch R. Microfluidic-based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in the sera of prostate cancer patients. Cancer Res 2011, 71:550-560.
54. White AK, VanInsberghe M, Petriv OI, Hamidi M, Sikorski D, Marra MA, Piret J, Aparicio S, Hansen CL. High-throughput microfluidic single-cell RT-qPCR. Proc Natl Acad Sci U S A 2011, 108:13999-14004.
55. Liu CG, Calin GA, Meloon B, Gamliel N, Sevignani C, Ferracin M, Dumitru CD, Shumizu M, Zupo S, Dono M, et al. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A 2004, 101:9740-9744.
56. Liu CG, Calin GA, Volinia S, Croce CM. MicroRNA expression profiling using microarrays. Nat Protoc 2008, 3:563-578.
57. Liu CG, Spizzo R, Calin GA, Croce CM. Expression profiling of microRNA using oligo DNA arrays. Methods 2008, 44:22-30.
58. Duan D, Zheng KX, Shen Y, Cao R, Jiang L, Lu Z, Yan X, Li J. Label-free high-throughput microRNA expression profiling from total RNA. Nucleic Acids Res 2011, 39:e154.
59. Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, Constantine-Paton M, Horvitz HR. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 2004, 5:R68.
60. Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z. Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 2004, 1:155-161.
61. Stahlberg A, Kubista M, Pfaffl M. Comparison of reverse transcriptases in gene expression analysis. Clin Chem 2004, 50:1678-1680.
62. Wang Y, Zheng D, Tan Q, Wang MX, Gu LQ. Nanopore-based detection of circulating microRNAs in lung cancer patients. Nat Nanotechnol 2011, 6:668-674.
63. Wanunu M, Dadosh T, Ray V, Jin J, McReynolds L, Drndic M. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nat Nanotechnol 2010, 5:807-814.
64. Bayley H, Jayasinghe L. Functional engineered channels and pores (review). Mol Membr Biol 2004, 21:209-220.
65. Gu LQ, Shim JW. Single molecule sensing by nanopores and nanopore devices. Analyst 2010, 135:441-451.
66. Howorka S, Siwy Z. Nanopore analytics: sensing of single molecules. Chem Soc Rev 2009, 38:2360-2384.
67. Movileanu L. Interrogating single proteins through nanopores: challenges and opportunities. Trends Biotechnol 2009, 27:333-341.
68. Ma L, Cockroft SL. Biological nanopores for single-molecule biophysics. Chembiochem 2010, 11:25-34.
69. Baker M. MicroRNA profiling: separating signal from noise. Nat Methods 2010, 7:687-692.
70. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007, 129:1401-1414.
71. Boeri M, Verri C, Conte D, Roz L, Modena P, Facchinetti F, Calabro E, Croce CM, Pastorino U, Sozzi G. MicroRNA signatures in tissues and plasma predict development and prognosis of computed tomography detected lung cancer. Proc Natl Acad Sci U S A 2011, 108:3713-3718.
72. Cortez MA, Calin GA. MicroRNA identification in plasma and serum: a new tool to diagnose and monitor diseases. Expert Opin Biol Ther 2009, 9:703-711.
73. Kroh EM, Parkin RK, Mitchell PS, Tewari M. Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 2010, 50:298-301.
74. Baccarini A, Chauhan H, Gardner TJ, Jayaprakash AD, Sachidanandam R, Brown BD. Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells. Curr Biol 2011, 21:369-376.
75. Baek D, Villen J, Shin C, Camargo FD, Gygi SP, Bartel DP. The impact of microRNAs on protein output. Nature 2008, 455:64-71.
76. Brown BD, Gentner B, Cantore A, Colleoni S, Amendola M, Zingale A, Baccarini A, Lazzari G, Galli C, Naldini L. Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state. Nat Biotechnol 2007, 25:1457-1467.
77. Brown BD, Naldini L. Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications. Nat Rev Genet 2009, 10:578-585.
78. Haley B, Zamore PD. Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol 2004, 11:599-606.
79. Hutvagner G, Zamore PD. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002, 297:2056-2060.
80. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455:58-63.
81. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 2008, 18:610-621.
82. Ebhardt HA, Fedynak A, Fahlman RP. Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity. Silence 2010, 1:12.
83. Lee LW, Zhang S, Etheridge A, Ma L, Martin D, Galas D, Wang K. Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 2010, 16:2170-2180.
84. Wu H, Ye C, Ramirez D, Manjunath N. Alternative processing of primary microRNA transcripts by Drosha generates 5′ end variation of mature microRNA. PLoS One 2009, 4:e7566.
85. Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, Fahlman RP. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 2009, 37:2461-2470.
86. Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R, Nishikura K. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 2006, 13:13-21.
87. Ehrenreich IM, Purugganan MD. Sequence variation of MicroRNAs and their binding sites in Arabidopsis. Plant Physiol 2008, 146:1974-1982.
88. Seitz H, Ghildiyal M, Zamore PD. Argonaute loading improves the 5′ precision of both MicroRNAs and their miRNA strands in flies. Curr Biol 2008, 18:147-151.
89. Kai ZS, Pasquinelli AE. MicroRNA assassins: factors that regulate the disappearance of miRNAs. Nat Struct Mol Biol 2010, 17:5-10.
90. Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 2001, 29:2549-2557.
91. Moltzahn F, Hunkapiller N, Mir AA, Imbar T, Blelloch R. High throughput microRNA profiling: optimized multiplex qRT-PCR at nanoliter scale on the fluidigm dynamic arrayTM IFCs. J Vis Exp 2011, 54:2552.
92. Zhou X, Zhu Q, Eicken C, Sheng N, Zhang X, Yang L, Gao X. MicroRNA profiling using microParaflo microfluidic array technology. Methods Mol Biol 2012, 822:153-182.
93. Chugh P, Tamburro K, Dittmer DP. Profiling of pre-micro RNAs and microRNAs using quantitative real-time PCR (qPCR) arrays. J Vis Exp 2010, 46:2210.
94. Kitchen RR, Kubista M, Tichopad A. Statistical aspects of quantitative real-time PCR experiment design. Methods 2010, 50:231-236.
95. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3:RESEARCH0034.
96. Kore AR, Hodeib M, Hu Z. Chemical synthesis of LNA-mCTP and its application for MicroRNA detection. Nucleosides Nucleotides Nucleic Acids 2008, 27:1-17.
97. Lock EF, Ziemiecke R, Marron J, Dittmer DP. Efficiency clustering for low-density microarrays and its application to QPCR. BMC Bioinform 2010, 11:386.
98. Pfaffl MW, Horgan GW, Dempfle L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 2002, 30:e36.
99. Tichopad A, Dilger M, Schwarz G, Pfaffl MW. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res 2003, 31:e122.
100. Meyer SU, Pfaffl MW, Ulbrich SE. Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity? Biotechnol Lett 2010, 32:1777-1788.
101. Peltier HJ, Latham GJ. Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 2008, 14:844-852.
102. Yang MC, Ruan QG, Yang JJ, Eckenrode S, Wu S, McIndoe RA, She JX. A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays. Physiol Genom 2001, 7:45-53.
103. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr Biol 2002, 12:735-739.
104. Kircher M, Kelso J. High-throughput DNA sequencing-concepts and limitations. Bioessays 2010, 32:524-536.
105. Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 2010, 24:992-1009.
106. Willenbrock H, Salomon J, Sokilde R, Barken KB, Hansen TN, Nielsen FC, Moller S, Litman T. Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA 2009, 15:2028-2034.
107. Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS. miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinform 2009, 10:328.
108. Tian G, Yin X, Luo H, Xu X, Bolund L, Zhang X, Gan SQ, Li N. Sequencing bias: comparison of different protocols of microRNA library construction. BMC Biotechnol 2010, 10:64.
109. Mestdagh P, Van Vlierberghe P, De Weer A, et al. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 2009, 10:R64.
110. Bissels U, Wild S, Tomiuk S, Holste A, Hafner M, Tuschl T, Bosio A. Absolute quantification of microRNAs by using a universal reference. RNA 2009, 15:2375-2384.
111. Newman MA, Mani V, Hammond SM. Deep sequencing of microRNA precursors reveals extensive 3′ end modification. RNA 2011, 17:1795-1803.