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
