Transposable Elements: Methods and Protocols (Methods in Molecular Biology, 2607) (in English)
Synopsis "Transposable Elements: Methods and Protocols (Methods in Molecular Biology, 2607) (in English)"
1. An overview of best practices for transposable element identification, classification and annotation in eukaryotic genomes Fernando Rodriguez and Irina R. Arkhipova 2. Assembly-free annotation and quantification of transposable elements with dnaPipeTE Clément Goubert 3. Best practice for the identification of horizontally transferred transposons James D Galbraith, Zhipeng Qu, Atma M Ivancevic, David L Adelson 4. Genotyping of transposable elements insertions segregating in the human populations using short-read re-alignments Xun Chen, Guillaume Bourque, and Clément Goubert 5. A Pangenome approach to detect and genotype TE insertion polymorphisms Cristian Groza, Guillaume Bourque, and Clément Goubert 6. Experimental validation of transposable element insertions using the Polymerase Chain Reaction (PCR) Miriam Merenciano, Marta Coronado-Zamora, and Josefa González 7. Quantification of LINE-1 RNA expression from bulk RNA-seq using L1EM Wilson McKerrow 8. Genome-wide profiling of L1 DNA methylation by bs-ATLAS-seq Claude Philippe and Gael Cristofari 9. Nanopore epigenomic analysis of transposable element DNA modifications Nathan Smits and Geoffrey Faulkner 10. Targeted resequencing and methylation analysis of L1 elements by nanopore sequencing Arpita Sarkar, Sophie Lanciano, and Gael Cristofari 11. Inferring protein-DNA binding profiles at interspersed repeats using HiChIP and PatChER Darren Taylor and Miguel R Branco 12. Affinity-based Interactome Analysis of Endogenous LINE-1 Macromolecules Luciano H. Di Stefano, Leila Saba, Mehrnoosh Oghbaie, Hua Jiang, Wilson McKerrow, Maria Benitez-Guijarro, Martin S. Taylor, and John LaCava 13. LINE-1 retrotransposition assays in embryonic stem cells Marta Garcia-Canadas, Francisco Sanchez-Luque, Laura Sanchez, Johana Rojas, and Jose Garcia Perez 14. Detecting somatic transposable element insertions in Drosophila tissues Katarzyna Siudeja 15. Precise and scarless insertion of transposable elements by Cas9-mediated genome engineering" Vivien M Weber, Aurelien J Doucet, and Gael Cristofari 16. Epigenetic editing of transposable and repetitive elements Joanna M Jachowicz 17. Using CRISPR to investigate the regulatory activity of transposable elements David M Simpson, Conor R Kelly, and Edward B Chuong
