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69. Moody L, He H, Pan YX, Chen H (2017) Methods and novel technology for microRNA
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70. Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP (2014) CAP-miRSeq: a
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71. Wu J, Liu Q, Wang X, Zheng J, Wang T, You M, Sheng Sun Z, Shi Q (2013) mirTools 2.0 for
non-coding RNA discovery, profiling, and functional annotation based on high-throughput
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72. Rueda A, Barturen G, Lebron R, Gomez-Martin C, Alganza A, Oliver JL, Hackenberg M
(2015) sRNAtoolbox: an integrated collection of small RNA research tools. Nucleic Acids Res
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73. Andres-Leon E, Nunez-Torres R, Rojas AM (2016) miARma-seq: a comprehensive tool for
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74. Garcia-Gimenez JL, Rubio-Belmar PA, Peiro-Chova L, Hervas D, Gonzalez-Rodriguez D,
Ibanez-Cabellos JS, Bas-Hermida P, Mena-Molla S, Garcia-Lopez EM, Pallardo FV, Bas T
(2018) Circulating miRNAs as diagnostic biomarkers for adolescent idiopathic scoliosis. Sci
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75. Gustafson D, Tyryshkin K, Renwick N (2016) microRNA-guided diagnostics in clinical
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beem.2016.07.002
76. Rodriguez M, Bajo-Santos C, Hessvik NP, Lorenz S, Fromm B, Berge V, Sandvig K, Line A,
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s12943-017-0726-4
77. Buschmann D, Kirchner B, Hermann S, Marte M, Wurmser C, Brandes F, Kotschote S,
Bonin M, Steinlein OK, Pfaffl MW, Schelling G, Reithmair M (2018) Evaluation of serum
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78. Van Ness J, Van Ness LK, Galas DJ (2003) Isothermal reactions for the amplification of
oligonucleotides. Proc Natl Acad Sci U S A 100(8):4504–4509. https://doi.org/10.1073/pnas.
0730811100
79. Zhang Y, Zhang CY (2012) Sensitive detection of microRNA with isothermal amplification and
a single-quantum-dot-based nanosensor. Anal Chem 84(1):224–231. https://doi.org/10.1021/
ac202405q
80. Liu H, Tian T, Zhang Y, Ding L, Yu J, Yan M (2017) Sensitive and rapid detection of
microRNAs using hairpin probes-mediated exponential isothermal amplification. Biosens
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81. Na J, Shin GW, Son HG, Lee SV, Jung GY (2017) Multiplex quantitative analysis of
microRNA expression via exponential isothermal amplification and conformation-sensitive
DNA separation. Sci Rep 7(1):11396. https://doi.org/10.1038/s41598-017-11895-6
82. Urbanek MO, Nawrocka AU, Krzyzosiak WJ (2015) Small RNA detection by in situ hybridization methods. Int J Mol Sci 16(6):13259–13286. https://doi.org/10.3390/ijms160613259
83. Thomas M, Lieberman J, Lal A (2010) Desperately seeking microRNA targets. Nat Struct Mol
Biol 17(10):1169–1174. https://doi.org/10.1038/nsmb.1921
84. Elmen J, Lindow M, Silahtaroglu A, Bak M, Christensen M, Lind-Thomsen A, Hedtjarn M,
Hansen JB, Hansen HF, Straarup EM, McCullagh K, Kearney P, Kauppinen S (2008) Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to
up-regulation of a large set of predicted target mRNAs in the liver. Nucleic Acids Res 36
(4):1153–1162. https://doi.org/10.1093/nar/gkm1113
Advanced Assays in Epigenetics
559
method for highly accurate miRNA quantification. Nucleic Acids Res 45(15):e144. https://doi.
org/10.1093/nar/gkx588
69. Moody L, He H, Pan YX, Chen H (2017) Methods and novel technology for microRNA
quantification in colorectal cancer screening. Clin Epigenetics 9:119. https://doi.org/10.1186/
s13148-017-0420-9
70. Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP (2014) CAP-miRSeq: a
comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics 15:423.
https://doi.org/10.1186/1471-2164-15-423
71. Wu J, Liu Q, Wang X, Zheng J, Wang T, You M, Sheng Sun Z, Shi Q (2013) mirTools 2.0 for
non-coding RNA discovery, profiling, and functional annotation based on high-throughput
sequencing. RNA Biol 10(7):1087–1092. https://doi.org/10.4161/rna.25193
72. Rueda A, Barturen G, Lebron R, Gomez-Martin C, Alganza A, Oliver JL, Hackenberg M
(2015) sRNAtoolbox: an integrated collection of small RNA research tools. Nucleic Acids Res
43(W1):W467–W473. https://doi.org/10.1093/nar/gkv555
73. Andres-Leon E, Nunez-Torres R, Rojas AM (2016) miARma-seq: a comprehensive tool for
miRNA, mRNA and circRNA analysis. Sci Rep 6:25749. https://doi.org/10.1038/srep25749
74. Garcia-Gimenez JL, Rubio-Belmar PA, Peiro-Chova L, Hervas D, Gonzalez-Rodriguez D,
Ibanez-Cabellos JS, Bas-Hermida P, Mena-Molla S, Garcia-Lopez EM, Pallardo FV, Bas T
(2018) Circulating miRNAs as diagnostic biomarkers for adolescent idiopathic scoliosis. Sci
Rep 8(1):2646. https://doi.org/10.1038/s41598-018-21146-x
75. Gustafson D, Tyryshkin K, Renwick N (2016) microRNA-guided diagnostics in clinical
samples. Best Pract Res Clin Endocrinol Metab 30(5):563–575. https://doi.org/10.1016/j.
beem.2016.07.002
76. Rodriguez M, Bajo-Santos C, Hessvik NP, Lorenz S, Fromm B, Berge V, Sandvig K, Line A,
Llorente A (2017) Identification of non-invasive miRNAs biomarkers for prostate cancer by
deep sequencing analysis of urinary exosomes. Mol Cancer 16(1):156. https://doi.org/10.1186/
s12943-017-0726-4
77. Buschmann D, Kirchner B, Hermann S, Marte M, Wurmser C, Brandes F, Kotschote S,
Bonin M, Steinlein OK, Pfaffl MW, Schelling G, Reithmair M (2018) Evaluation of serum
extracellular vesicle isolation methods for profiling miRNAs by next-generation sequencing.
J Extracell Vesicles 7(1):1481321. https://doi.org/10.1080/20013078.2018.1481321
78. Van Ness J, Van Ness LK, Galas DJ (2003) Isothermal reactions for the amplification of
oligonucleotides. Proc Natl Acad Sci U S A 100(8):4504–4509. https://doi.org/10.1073/pnas.
0730811100
79. Zhang Y, Zhang CY (2012) Sensitive detection of microRNA with isothermal amplification and
a single-quantum-dot-based nanosensor. Anal Chem 84(1):224–231. https://doi.org/10.1021/
ac202405q
80. Liu H, Tian T, Zhang Y, Ding L, Yu J, Yan M (2017) Sensitive and rapid detection of
microRNAs using hairpin probes-mediated exponential isothermal amplification. Biosens
Bioelectron 89(Pt 2):710–714. https://doi.org/10.1016/j.bios.2016.10.099
81. Na J, Shin GW, Son HG, Lee SV, Jung GY (2017) Multiplex quantitative analysis of
microRNA expression via exponential isothermal amplification and conformation-sensitive
DNA separation. Sci Rep 7(1):11396. https://doi.org/10.1038/s41598-017-11895-6
82. Urbanek MO, Nawrocka AU, Krzyzosiak WJ (2015) Small RNA detection by in situ hybridization methods. Int J Mol Sci 16(6):13259–13286. https://doi.org/10.3390/ijms160613259
83. Thomas M, Lieberman J, Lal A (2010) Desperately seeking microRNA targets. Nat Struct Mol
Biol 17(10):1169–1174. https://doi.org/10.1038/nsmb.1921
84. Elmen J, Lindow M, Silahtaroglu A, Bak M, Christensen M, Lind-Thomsen A, Hedtjarn M,
Hansen JB, Hansen HF, Straarup EM, McCullagh K, Kearney P, Kauppinen S (2008) Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to
up-regulation of a large set of predicted target mRNAs in the liver. Nucleic Acids Res 36
(4):1153–1162. https://doi.org/10.1093/nar/gkm1113
Advanced Assays in Epigenetics
559