High-Throughput Nuclease Probing of RNA Structures Using FragSeq.
暂无分享,去创建一个
[1] Andrew Fire,et al. Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans , 2007, Science.
[2] A. Maxam,et al. Structure mapping of 5'-32P-labeled RNA with S1 nuclease. , 1978, Biochemistry.
[3] Manolis Kellis,et al. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo , 2013, Nature.
[4] R. Sachidanandam,et al. Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing , 2011, Nucleic acids research.
[5] S. Oliviero,et al. Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome , 2014, Genome Biology.
[6] Steven Busan,et al. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) , 2014, Nature Methods.
[7] K. Weeks. Advances in RNA structure analysis by chemical probing. , 2010, Current opinion in structural biology.
[8] J. Ebel,et al. Probing the structure of RNAs in solution. , 1987, Nucleic acids research.
[9] G. Hannon,et al. Preparation of small RNA libraries for high-throughput sequencing. , 2012, Cold Spring Harbor protocols.
[10] J. Sambrook,et al. Molecular Cloning: A Laboratory Manual , 2001 .
[11] L. Stein,et al. JBrowse: a next-generation genome browser. , 2009, Genome research.
[12] Kevin M Weeks,et al. Structure-independent and quantitative ligation of single-stranded DNA. , 2006, Analytical biochemistry.
[13] J. Lingner,et al. 3'-end labeling of RNA with recombinant yeast poly(A) polymerase. , 1993, Nucleic acids research.
[14] Nikolay V. Dokholyan,et al. Single-molecule correlated chemical probing of RNA , 2014, Proceedings of the National Academy of Sciences.
[15] Stuart Aitken,et al. Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution , 2014, Nucleic acids research.
[16] Y. Zhang,et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features , 2013, Nature.
[17] D. Draper,et al. On the recognition of helical RNA by cobra venom V1 nuclease. , 1986, The Journal of biological chemistry.
[18] O. Uhlenbeck,et al. Reactions at the termini of tRNA with T4 RNA ligase. , 1978, Nucleic acids research.
[19] O. Uhlenbeck,et al. 3'-Phosphatase activity in T4 polynucleotide kinase. , 1977, Biochemistry.
[20] D. Haussler,et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing , 2010, Nature Methods.
[21] D. Mathews,et al. Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.
[22] A. Krogh,et al. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. , 2015, RNA.
[23] Nuno A. Fonseca,et al. Tools for mapping high-throughput sequencing data , 2012, Bioinform..
[24] P. Chomczyński,et al. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.
[25] A. Rich,et al. Comparison of transfer ribonucleic acid structures using cobra venom and S1 endonucleases. , 1982, Biochemistry.
[26] S. Fields,et al. Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates. , 2010, RNA.
[27] J. Woolford,et al. Mod-seq: high-throughput sequencing for chemical probing of RNA structure , 2014, RNA.
[28] David H. Mathews,et al. RNAstructure: software for RNA secondary structure prediction and analysis , 2010, BMC Bioinformatics.
[29] Paul Ryvkin,et al. Global analysis of RNA secondary structure in two metazoans. , 2012, Cell reports.
[30] Trinucleotide repeat system for sequence specificity analysis of RNA structure probing reagents. , 2010, Analytical biochemistry.
[31] Nikolaos Sidiropoulos,et al. Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools. , 2015, Methods in enzymology.
[32] Rhiju Das,et al. Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol. , 2013, Methods in molecular biology.
[33] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[34] J. Doudna,et al. Insights into RNA structure and function from genome-wide studies , 2014, Nature Reviews Genetics.
[35] Cole Trapnell,et al. Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) , 2011, Proceedings of the National Academy of Sciences.
[36] Spitale Robert,et al. Structural imprints in vivo decode RNA regulatory mechanisms , 2016 .
[37] Alice Carolyn McHardy,et al. Allele dynamics plots for the study of evolutionary dynamics in viral populations , 2010, Nucleic Acids Res..
[38] Lukasz Jan Kielpinski,et al. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility , 2014, Nucleic acids research.
[39] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[40] Yann Ponty,et al. VARNA: Interactive drawing and editing of the RNA secondary structure , 2009, Bioinform..
[41] G. Fox,et al. Secondary structure of eukaryotic cytoplasmic 5S ribosomal RNA. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[42] A. Sandelin,et al. Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing. , 2013, Methods in molecular biology.
[43] Yin Tang,et al. The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. , 2015, Trends in biochemical sciences.
[44] Ravinder Singh,et al. Gamma-monomethyl phosphate: a cap structure in spliceosomal U6 small nuclear RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[45] Jernej Ule,et al. hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1 , 2015, Nature.
[46] S. Fields,et al. Stanley Fields phosphates-cyclic ′ , 3 ′ Capture and sequence analysis of RNAs with terminal 2 Material Supplemental , 2010 .