Library Construction for High-Throughput Mobile Element Identification and Genotyping
作者： Hongseok Ha , Nan Wang , Jinchuan Xing
关键词: Mobile genetic elements 、 Computational analysis 、 Genetics 、 Genome 、 DNA sequencing 、 Biology 、 Genotyping 、 Computational biology 、 Oligonucleotide 、 Population diversity
摘要: Mobile genetic elements are discrete DNA that can move around and copy themselves in a genome. As ubiquitous component of the genome, mobile contribute to both epigenetic variation. Therefore, it is important determine genome-wide distribution elements. Here we present targeted high-throughput sequencing protocol called Element Scanning (ME-Scan) for element detection. We will describe oligonucleotides design, library construction, computational analysis ME-Scan protocol.
springer.com
sci-hub.se 参考文章(31)
J. K. Pace, C. Feschotte, The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage Genome Research. ,vol. 17, pp. 422- 432 ,(2007) , 10.1101/GR.5826307
Kenji Ichiyanagi, Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs Genes & Genetic Systems. ,vol. 88, pp. 19- 29 ,(2013) , 10.1266/GGS.88.19
Matthew H Wilson, Craig J Coates, Alfred L George, PiggyBac Transposon-Mediated Gene Transfer in Human Cells Molecular Therapy. ,vol. 15, pp. 139- 145 ,(2007) , 10.1038/SJ.MT.6300028
Kathleen H. Burns, Jef D. Boeke, Human transposon tectonics. Cell. ,vol. 149, pp. 740- 752 ,(2012) , 10.1016/J.CELL.2012.04.019
Michael Cowley, Rebecca J. Oakey, Transposable Elements Re-Wire and Fine-Tune the Transcriptome PLOS Genetics. ,vol. 9, ,(2013) , 10.1371/JOURNAL.PGEN.1003234
Cheng Ran Lisa Huang, Anna M. Schneider, Yunqi Lu, Tejasvi Niranjan, Peilin Shen, Matoya A. Robinson, Jared P. Steranka, David Valle, Curt I. Civin, Tao Wang, Sarah J. Wheelan, Hongkai Ji, Jef D. Boeke, Kathleen H. Burns, Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome Cell. ,vol. 141, pp. 1171- 1182 ,(2010) , 10.1016/J.CELL.2010.05.026
Wan-Ping Lee, Michael P. Stromberg, Alistair Ward, Chip Stewart, Erik P. Garrison, Gabor T. Marth, MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping PLoS ONE. ,vol. 9, pp. e90581- ,(2014) , 10.1371/JOURNAL.PONE.0090581
Christine R. Beck, Pamela Collier, Catriona Macfarlane, Maika Malig, Jeffrey M. Kidd, Evan E. Eichler, Richard M. Badge, John V. Moran, LINE-1 Retrotransposition Activity in Human Genomes Cell. ,vol. 141, pp. 1159- 1170 ,(2010) , 10.1016/J.CELL.2010.05.021
Christel Rouget, Catherine Papin, Anthony Boureux, Anne-Cécile Meunier, Bénédicte Franco, Nicolas Robine, Eric C. Lai, Alain Pelisson, Martine Simonelig, Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo Nature. ,vol. 467, pp. 1128- 1132 ,(2010) , 10.1038/NATURE09465
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2