TY - JOUR AU - Witwer, K. W. AU - Halushka, M. K. PY - 2016 DA - 2016// TI - Toward the promise of microRNAs - enhancing reproducibility and rigor in microRNA research JO - RNA Biol VL - 13 UR - https://doi.org/10.1080/15476286.2016.1236172 DO - 10.1080/15476286.2016.1236172 ID - Witwer2016 ER - TY - JOUR AU - Pritchard, C. C. AU - Cheng, H. H. AU - Tewari, M. PY - 2012 DA - 2012// TI - MicroRNA profiling: approaches and considerations JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3198 DO - 10.1038/nrg3198 ID - Pritchard2012 ER - TY - JOUR AU - Linsen, S. E. AU - de Wit, E. AU - Janssens, G. AU - Heater, S. AU - Chapman, L. AU - Parkin, R. K. AU - Fritz, B. AU - Wyman, S. K. AU - de Bruijn, E. AU - Voest, E. E. PY - 2009 DA - 2009// TI - Limitations and possibilities of small RNA digital gene expression profiling JO - Nat Methods VL - 6 UR - https://doi.org/10.1038/nmeth0709-474 DO - 10.1038/nmeth0709-474 ID - Linsen2009 ER - TY - JOUR AU - Tian, G. AU - Yin, X. AU - Luo, H. AU - Xu, X. AU - Bolund, L. AU - Zhang, X. AU - Gan, S. Q. AU - Li, N. PY - 2010 DA - 2010// TI - Sequencing bias: comparison of different protocols of microRNA library construction JO - BMC Biotechnol VL - 10 UR - https://doi.org/10.1186/1472-6750-10-64 DO - 10.1186/1472-6750-10-64 ID - Tian2010 ER - TY - JOUR AU - Hafner, M. AU - Renwick, N. AU - Brown, M. AU - Mihailovic, A. AU - Holoch, D. AU - Lin, C. AU - Pena, J. T. AU - Nusbaum, J. D. AU - Morozov, P. AU - Ludwig, J. PY - 2011 DA - 2011// TI - RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries JO - RNA VL - 17 UR - https://doi.org/10.1261/rna.2799511 DO - 10.1261/rna.2799511 ID - Hafner2011 ER - TY - JOUR AU - McCormick, K. P. AU - Willmann, M. R. AU - Meyers, B. C. PY - 2011 DA - 2011// TI - Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments JO - Silence VL - 2 UR - https://doi.org/10.1186/1758-907X-2-2 DO - 10.1186/1758-907X-2-2 ID - McCormick2011 ER - TY - JOUR AU - Sorefan, K. AU - Pais, H. AU - Hall, A. E. AU - Kozomara, A. AU - Griffiths-Jones, S. AU - Moulton, V. AU - Dalmay, T. PY - 2012 DA - 2012// TI - Reducing ligation bias of small RNAs in libraries for next generation sequencing JO - Silence VL - 3 UR - https://doi.org/10.1186/1758-907X-3-4 DO - 10.1186/1758-907X-3-4 ID - Sorefan2012 ER - TY - JOUR AU - Fuchs, R. T. AU - Sun, Z. AU - Zhuang, F. AU - Robb, G. B. PY - 2015 DA - 2015// TI - Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0126049 DO - 10.1371/journal.pone.0126049 ID - Fuchs2015 ER - TY - STD TI - Bicalho Saturnino G, Godinho CPS, Fagundes-Lima D, Silva AC, Weber G. Detection of construction biases in biological databases: the case of miRBase. In: ArXiv e-prints; 2014. https://arxiv.org/abs/1407.6570. UR - https://arxiv.org/abs/1407.6570 ID - ref9 ER - TY - JOUR AU - Jayaprakash, A. D. AU - Jabado, O. AU - Brown, B. D. AU - Sachidanandam, R. PY - 2011 DA - 2011// TI - Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr693 DO - 10.1093/nar/gkr693 ID - Jayaprakash2011 ER - TY - JOUR AU - Zhuang, F. AU - Fuchs, R. T. AU - Sun, Z. AU - Zheng, Y. AU - Robb, G. B. PY - 2012 DA - 2012// TI - Structural bias in T4 RNA ligase-mediated 3′-adapter ligation JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1263 DO - 10.1093/nar/gkr1263 ID - Zhuang2012 ER - TY - JOUR AU - Zhuang, F. AU - Fuchs, R. T. AU - Robb, G. B. PY - 2012 DA - 2012// TI - Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation JO - J Nucleic Acids VL - 2012 UR - https://doi.org/10.1155/2012/360358 DO - 10.1155/2012/360358 ID - Zhuang2012 ER - TY - JOUR AU - Raabe, C. A. AU - Tang, T. H. AU - Brosius, J. AU - Rozhdestvensky, T. S. PY - 2014 DA - 2014// TI - Biases in small RNA deep sequencing data JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1021 DO - 10.1093/nar/gkt1021 ID - Raabe2014 ER - TY - JOUR AU - Baran-Gale, J. AU - Kurtz, C. L. AU - Erdos, M. R. AU - Sison, C. AU - Young, A. AU - Fannin, E. E. AU - Chines, P. S. AU - Sethupathy, P. PY - 2015 DA - 2015// TI - Addressing Bias in small RNA library preparation for sequencing: a new protocol recovers MicroRNAs that evade capture by current methods JO - Front Genet VL - 6 UR - https://doi.org/10.3389/fgene.2015.00352 DO - 10.3389/fgene.2015.00352 ID - Baran-Gale2015 ER - TY - JOUR AU - Kozomara, A. AU - Griffiths-Jones, S. PY - 2014 DA - 2014// TI - miRBase: annotating high confidence microRNAs using deep sequencing data JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1181 DO - 10.1093/nar/gkt1181 ID - Kozomara2014 ER - TY - JOUR AU - Dard-Dascot, C. AU - Naquin, D. AU - d'Aubenton-Carafa, Y. AU - Alix, K. AU - Thermes, C. AU - van Dijk, E. PY - 2018 DA - 2018// TI - Systematic comparison of small RNA library preparation protocols for next-generation sequencing JO - BMC Genomics VL - 19 UR - https://doi.org/10.1186/s12864-018-4491-6 DO - 10.1186/s12864-018-4491-6 ID - Dard-Dascot2018 ER - TY - JOUR AU - Yang, Q. AU - Hua, J. AU - Wang, L. AU - Xu, B. AU - Zhang, H. AU - Ye, N. AU - Zhang, Z. AU - Yu, D. AU - Cooke, H. J. AU - Zhang, Y. AU - Shi, Q. PY - 2013 DA - 2013// TI - MicroRNA and piRNA profiles in normal human testis detected by next generation sequencing JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0066809 DO - 10.1371/journal.pone.0066809 ID - Yang2013 ER - TY - JOUR AU - Chugh, P. AU - Dittmer, D. P. PY - 2012 DA - 2012// TI - Potential pitfalls in microRNA profiling JO - Wiley Interdiscip Rev RNA VL - 3 UR - https://doi.org/10.1002/wrna.1120 DO - 10.1002/wrna.1120 ID - Chugh2012 ER - TY - JOUR AU - Mestdagh, P. AU - Hartmann, N. AU - Baeriswyl, L. AU - Andreasen, D. AU - Bernard, N. AU - Chen, C. AU - Cheo, D. AU - D'Andrade, P. AU - DeMayo, M. AU - Dennis, L. PY - 2014 DA - 2014// TI - Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study JO - Nat Methods VL - 11 UR - https://doi.org/10.1038/nmeth.3014 DO - 10.1038/nmeth.3014 ID - Mestdagh2014 ER - TY - JOUR AU - Moldovan, L. AU - Batte, K. E. AU - Trgovcich, J. AU - Wisler, J. AU - Marsh, C. B. AU - Piper, M. PY - 2014 DA - 2014// TI - Methodological challenges in utilizing miRNAs as circulating biomarkers JO - J Cell Mol Med VL - 18 UR - https://doi.org/10.1111/jcmm.12236 DO - 10.1111/jcmm.12236 ID - Moldovan2014 ER - TY - JOUR AU - Tam, S. AU - de Borja, R. AU - Tsao, M. S. AU - McPherson, J. D. PY - 2014 DA - 2014// TI - Robust global microRNA expression profiling using next-generation sequencing technologies JO - Lab Investig VL - 94 UR - https://doi.org/10.1038/labinvest.2013.157 DO - 10.1038/labinvest.2013.157 ID - Tam2014 ER - TY - JOUR AU - Backes, C. AU - Sedaghat-Hamedani, F. AU - Frese, K. AU - Hart, M. AU - Ludwig, N. AU - Meder, B. AU - Meese, E. AU - Keller, A. PY - 2016 DA - 2016// TI - Bias in high-throughput analysis of miRNAs and implications for biomarker studies JO - Anal Chem VL - 88 UR - https://doi.org/10.1021/acs.analchem.5b03376 DO - 10.1021/acs.analchem.5b03376 ID - Backes2016 ER - TY - JOUR AU - Leshkowitz, D. AU - Horn-Saban, S. AU - Parmet, Y. AU - Feldmesser, E. PY - 2013 DA - 2013// TI - Differences in microRNA detection levels are technology and sequence dependent JO - RNA VL - 19 UR - https://doi.org/10.1261/rna.036475.112 DO - 10.1261/rna.036475.112 ID - Leshkowitz2013 ER - TY - JOUR AU - Tosar, J. P. AU - Rovira, C. AU - Naya, H. AU - Cayota, A. PY - 2014 DA - 2014// TI - Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS JO - RNA VL - 20 UR - https://doi.org/10.1261/rna.044263.114 DO - 10.1261/rna.044263.114 ID - Tosar2014 ER - TY - JOUR AU - Kwon, Y. S. PY - 2011 DA - 2011// TI - Small RNA library preparation for next-generation sequencing by single ligation, extension and circularization technology JO - Biotechnol Lett VL - 33 UR - https://doi.org/10.1007/s10529-011-0611-y DO - 10.1007/s10529-011-0611-y ID - Kwon2011 ER - TY - STD TI - Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp. 2011;(50). https://doi.org/10.3791/2638. ID - ref26 ER - TY - JOUR AU - Lamm, A. T. AU - Stadler, M. R. AU - Zhang, H. AU - Gent, J. I. AU - Fire, A. Z. PY - 2011 DA - 2011// TI - Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.108845.110 DO - 10.1101/gr.108845.110 ID - Lamm2011 ER - TY - JOUR AU - Ingolia, N. T. AU - Brar, G. A. AU - Rouskin, S. AU - McGeachy, A. M. AU - Weissman, J. S. PY - 2012 DA - 2012// TI - The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2012.086 DO - 10.1038/nprot.2012.086 ID - Ingolia2012 ER - TY - JOUR AU - Jackson, T. J. AU - Spriggs, R. V. AU - Burgoyne, N. J. AU - Jones, C. AU - Willis, A. E. PY - 2014 DA - 2014// TI - Evaluating bias-reducing protocols for RNA sequencing library preparation JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-569 DO - 10.1186/1471-2164-15-569 ID - Jackson2014 ER - TY - JOUR AU - Heyer, E. E. AU - Ozadam, H. AU - Ricci, E. P. AU - Cenik, C. AU - Moore, M. J. PY - 2015 DA - 2015// TI - An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1235 DO - 10.1093/nar/gku1235 ID - Heyer2015 ER - TY - JOUR AU - Sterling, C. H. AU - Veksler-Lublinsky, I. AU - Ambros, V. PY - 2015 DA - 2015// TI - An efficient and sensitive method for preparing cDNA libraries from scarce biological samples JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku637 DO - 10.1093/nar/gku637 ID - Sterling2015 ER - TY - JOUR AU - Brennan, C. A. AU - Manthey, A. E. AU - Gumport, R. I. PY - 1983 DA - 1983// TI - Using T4 RNA ligase with DNA substrates JO - Methods Enzymol VL - 100 UR - https://doi.org/10.1016/0076-6879(83)00044-0 DO - 10.1016/0076-6879(83)00044-0 ID - Brennan1983 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Chung, I. F. AU - Chang, S. J. AU - Chen, C. Y. AU - Liu, S. H. AU - Li, C. Y. AU - Chan, C. H. AU - Shih, C. C. AU - Cheng, W. C. PY - 2017 DA - 2017// TI - YM500v3: a database for small RNA sequencing in human cancer research JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1084 DO - 10.1093/nar/gkw1084 ID - Chung2017 ER - TY - STD TI - Barberan-Soler S, Kazakov SA: Increasing miRNA sequencing accuracy using an RNA circularization approach. NCBI GEO. Datasets. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107304. UR - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107304 ID - ref35 ER - TY - JOUR AU - Kumar, P. AU - Johnston, B. H. AU - Kazakov, S. A. PY - 2011 DA - 2011// TI - miR-ID: a novel, circularization-based platform for detection of microRNAs JO - RNA VL - 17 UR - https://doi.org/10.1261/rna.2490111 DO - 10.1261/rna.2490111 ID - Kumar2011 ER -