mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets

References

• Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162:156–9.
   PubMed Web of Science ®Google Scholar
• Chomczynski P, Sacchi N. The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat Protoc. 2006;1:581.
   PubMed Web of Science ®Google Scholar
• Zeugin JA, Hartley JL. Ethanol precipitation of DNA. Focus. 1985;7:1–2.
   Google Scholar
• Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. BioMed Res Int. 2009;574398:1–10.
   Google Scholar
• Hennion M-C. Solid-phase extraction: method development, sorbents, and coupling with liquid chromatography. J Chromatogr A. 1999;856:3–54.
   PubMed Web of Science ®Google Scholar
• Augusto F, Hantao LW, Mogollon NG, et al. New materials and trends in sorbents for solid-phase extraction. TrAC Trends Anal Chem. 2013;43:14–23.
   Web of Science ®Google Scholar
• Esser K-H, Marx WH, Lisowsky T. Nucleic acid-free matrix: regeneration of DNA binding columns. Biotechniques. 2005;39:270–1.
   Web of Science ®Google Scholar
• Gjerde DT, Hoang L, Hornby D. RNA purification and analysis: sample preparation, extraction, chromatography. Hoboken, (NY): John Wiley & Sons; 2009.
   Google Scholar
• Sun N, Deng C, Liu Y, et al. Optimization of influencing factors of nucleic acid adsorption onto silica-coated magnetic particles: application to viral nucleic acid extraction from serum. J Chromatogr A. 2014;1325:31–9.
   PubMed Web of Science ®Google Scholar
• Nargessi RD. CB, Inc. Magnetic isolation and purification of nucleic acids. United States patent US 6855499 B1. 2005.
   Google Scholar
• Cseke LJ, Kirakosyan A, Kaufman PB, et al. Handbook of molecular and cellular methods in biology and medicine. Boca Raton, (FL): CRC press; 2011.
   Google Scholar
• Ivey KN, Srivastava D. MicroRNAs as regulators of differentiation and cell fate decisions. Cell Stem Cell. 2010;7:36–41.
   PubMed Web of Science ®Google Scholar
• Ivey KN, Srivastava D. microRNAs as developmental regulators. Cold Spring Harb Perspect Biol. 2015;7:a008144.
   PubMed Web of Science ®Google Scholar
• Allegra A, Alonci A, Campo S, et al. Circulating microRNAs: new biomarkers in diagnosis, prognosis and treatment of cancer (review). Int J Oncol. 2012;41:1897–912.
   PubMed Web of Science ®Google Scholar
• Lan H, Lu H, Wang X, et al. MicroRNAs as potential biomarkers in cancer: opportunities and challenges. BioMed Res Int. 2015;125094:1–17.
   Google Scholar
• Jansson MD, Lund AH. MicroRNA and cancer. Mol Oncol. 2012;6:590–610.
   PubMed Web of Science ®Google Scholar
• Walleshauser III JG, Kessler T, Morse D, Tannous BA, Chiu NH. A simple approach for evaluating total MicroRNA extraction from mouse brain tissues. 2012.
   Google Scholar
• Zhang J, Li S, Li L, et al. Exosome and exosomal microRNA: trafficking, sorting, and function. Genomics, Proteomics & Bioinformatics. 2015;13:17–24.
   PubMed Web of Science ®Google Scholar
• Castoldi M, Benes V, Hentze MW, et al. miChip: a microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture probes. Methods. 2007;43:146–52.
   PubMed Web of Science ®Google Scholar
• Aravin A, Tuschl T. Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett. 2005;579:5830–40.
   PubMed Web of Science ®Google Scholar
• Raza K, Ahmad S. Principle, analysis, application and challenges of next-generation sequencing: a review. arXiv preprint arXiv:160605254. 2016.
   Google Scholar
• Berezikov E, Cuppen E, Plasterk RH. Approaches to microRNA discovery. Nat Genet. 2006;38:S2–S7.
   PubMed Web of Science ®Google Scholar
• Pall GS, Hamilton AJ. Improved northern blot method for enhanced detection of small RNA. Nat Protoc. 2008;3:1077–84.
   PubMed Web of Science ®Google Scholar
• Jiang J, Lee EJ, Gusev Y, et al. Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res. 2005;33:5394–403.
   PubMed Web of Science ®Google Scholar
• Ryu S, McDonnell K, Choi H, et al. Suppression of miRNA-708 by polycomb group promotes metastases by calcium-induced cell migration. Cancer Cell. 2013;23:63–76.
   PubMed Web of Science ®Google Scholar
• Cech TR, Steitz JA. The noncoding RNA revolution—trashing old rules to forge new ones. Cell. 2014;157:77–94.
   PubMed Web of Science ®Google Scholar
• Tang F, Hajkova P, Barton SC, et al. MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res. 2006;34:e9–e.
   PubMed Web of Science ®Google Scholar
• Nilsen TW. Removing rRNA from deproteinized, phenol-extracted total RNA by enzymatic digestion. Cold Spring Harb Protoc. 2012;2012:pdb. prot072124.
   PubMedGoogle Scholar
• Rio DC, Ares M, Hannon GJ, et al. Purification of RNA by SDS solubilization and phenol extraction. Cold Spring Harb Protoc. 2010;2010:pdb. prot5438.
   PubMedGoogle Scholar
• Rio DC, Ares M, Hannon GJ, et al. Removal of ribosomal subunits (and rRNA) from cytoplasmic extracts before solubilization with SDS and deproteinization. Cold Spring Harb Protoc. 2010;2010:pdb. prot5442.
   PubMedGoogle Scholar
• Rio DC, Ares M, Hannon GJ, et al. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harb Protoc. 2010;2010:pdb. prot5439.
   PubMedGoogle Scholar
• Ambros V. The functions of animal microRNAs. Nature. 2004;431:350.
   PubMed Web of Science ®Google Scholar
• Ma F, Li W, Liu C, et al. MiR-23a promotes TGF-β1-induced EMT and tumor metastasis in breast cancer cells by directly targeting CDH1 and activating Wnt/β-catenin signaling. Oncotarget. 2017;8:69538–69550.
   PubMedGoogle Scholar
• Liu H, Pan Y, Han X, et al. MicroRNA-216a promotes the metastasis and epithelial–mesenchymal transition of ovarian cancer by suppressing the PTEN/AKT pathway. OncoTargets Ther. 2017;10:2701.
   PubMed Web of Science ®Google Scholar
• Zhang D, Zhao L, Shen Q, et al. Down‐regulation of KIAA1199/CEMIP by miR‐216a suppresses tumor invasion and metastasis in colorectal cancer. Int J Cancer. 2017;140:2298–309.
   PubMed Web of Science ®Google Scholar
• Xia H, Ooi LLP, Hui KM. MicroRNA‐216a/217‐induced epithelial‐mesenchymal transition targets PTEN and SMAD7 to promote drug resistance and recurrence of liver cancer. Hepatology. 2013;58:629–41.
   PubMed Web of Science ®Google Scholar
• Summer H, Grämer R, Dröge P. Denaturing urea polyacrylamide gel electrophoresis (Urea PAGE). J Vis Exp: JoVE. 2009;32:1485.
   Google Scholar
• Gardner PP, Daub J, Tate JG, et al. Rfam: updates to the RNA families database. Nucleic Acids Res. 2008;37:D136–D40.
   PubMed Web of Science ®Google Scholar
• Griffiths-Jones S. miRBase: the microRNA sequence database. MicroRNA Protoc. 2006;342:129–38.
   Google Scholar