Transposable Elements Methods and Protocols Methods in Molecular Biology 2607

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