Protocols

Protocol name	Programs	TE analysis	TE type	Protocol link	Model(s)	Year
De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue	REPET	large genome TE annotation	all TE	Jamilloux et al., 2017	Plants	2017
SCIFER: : approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution	cellranger, bowtie1	Single-Cell RNA-seq	LINE1	Stow et al., 2022	human, mouse	2022
Curation Guidelines for de novo Generated Transposable Element Families	alignAndCallConsensus, ClusterPartialMatchingSubs, AutoRunBlocker	curation, subfamily analaysis	all TE	Storer et al. 2021	Mammalia	2021
Mining of Miniature Transposable Elements in Brassica Species at BrassicaTED	BrassicaTED	database search	MITE	Jayakodi et al., 2021	Plants, Brassica	2021
Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq	ALE-seq	high-throughput identification of novel LTR	LTR	Wang et al., 2021	Plants	2021
Detection of Transposition Events from Next-Generation Sequencing Data	TIF	insertion polymorphism	All TE with TSD	Miyao 2021	---	2021
Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data	SPLITREADER, TEPID	insertion polymorphism	all TE	Baduel et al., 2021	Plants	2021
Detecting Signatures of TE Polymorphisms in Short-Read Sequencing Data	Detettore	insertion polymorphism	all TE	Stritt et al., 2021	Plants, Brachypodium	2021
A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants	LTRpred	functional annotation	LTR	Benoit et al., 2021	Plants	2021
In Silico Identification of Stress-Associated Transposable Elements in Arabidopsis thaliana Using Public Transcriptome Data	StringTie, edgeR	differential expression	all TE	Doğa et al. 2021	---	2021
A Tutorial of EDTA: Extensive De Novo TE Annotator	EDTA	de novo repeat identification from genome assembly	all TE	Su et al. 2021	---	2021
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2	RepeatExplorer2	in silico repeat identification by read clustering	all TE	Novák et al. 2020	---	2020
An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes	Multiple	TE identification, annotation, classification,	all TE	Rodriguez and Arkhipova., 2022	All	2022
Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE	dnaPipeTE	TE annotation and quantification from short-reads	all TE	Goubert 2022	All	2022
Detecting Horizontal Transfer of Transposons	Multiple	Detection of HTT	all TE	Galbraith et al., 2022	All	2022
Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments	ERVcaller, MELT2, TypeREF	Insertion Polymorphisms	Alu, L1, SVA, HERV	Chen et al., 2022	Mammal	2022
A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms	Multiple	insertion polymorphism, pangenome	Alu, L1, SVA	Groza et al., 2022	Mammal	2022
Quantification of LINE-1 RNA Expression from Bulk RNA-seq Using L1EM	L1EM	Bulk, locus-specific RNA-seq	LINE-1	McKerrow 2022	---	2022

Protocol name	Method name	TE analysis	TE type	Protocol link	Model(s)	Year
Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture	Sequence Capture	insertion polymorphism	all TE	Quadrana et al., 2021	Plants, Arabidopsis	2021
Genome-Wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing		targeted high-throughput sequencing	MITE	Tang et al., 2021	Plants, Rice	2021
Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq	Mobilome-Seq	active DNA transposons and retrotransposons	Extrachromosomal Circular TE	Tang et al., 2021	Plants	2021
Identification of Active Transposable Elements in Plants: The Mobilome-Seq Approach	Mobilome-Seq	active DNA transposons and retrotransposons	Retrotransposons	Thieme et al., 2021	Plants	2021
High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq	ALE-seq	high-throughput identification of novel LTR	LTR	Wang et al., 2021	Plants	2021
Determination of TE Insertion Positions Using Transposon Display	Transposon Display	insertion polymorphism	Retrotransposons	Kim et al., 2021	Plants	2021
Quantitative Measurement of Transposon Copy Number Using the Droplet Digital PCR	ddPCR	copy number variation	Retrotransposons, EVADE	Fan et al., 2021	Plants, Arabidopsis	2021
Measurement of Genetic Mobility Using a Transposon-Based Marker System in Sorghum	TE-TRAP	PCR-based marker	PIF/Harbinger	Stritt et al., 2021	Plants, Sorghum	2021
Sequence-Specific Amplified Polymorphism (SSAP) and Sequence Characterized Amplified Region (SCAR) Markers in Zea mays	Sequence-specific amplified polymorphism (SSAP), Sequence characterized amplified region (SCAR)	insertion polymorphism	LTR	Roy et al., 2021	Plants, Maize	2021
Experimental Validation of Transposable Element Insertions Using the Polymerase Chain Reaction (PCR)	Citizen Fly Lab	insertion polymorphism	All	Merenciano et al., 2022	Drosophila	2022
Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq	bs-ATLAS-seq	Methylation Profiling	L1HS	Philippe and Cristofari, 2022	human	2022
Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications	---	targeted long-read sequencing, insertion polymorphism, 5mC methylation	All (L1 as example)	Smits and Faulkner, 2022	All	2022
Inferring Protein-DNA Binding Profiles at Interspersed Repeats Using HiChIP and PAtChER	HiChIP, PAtChER	ChIP-seq, Hi-C, protein binding profiling	All	Taylor and Branco, 2022	All	2022
Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules	---	Affinity capture, Protein complexes, Interactomics	LINE-1	Di Stefano et al., 2022	---	2022
LINE-1 Retrotransposition Assays in Embryonic Stem Cells	---	Retrotransposition assay	LINE-1, Alu	Di Stefano et al., 2022	human, mice	2022
Experimental Approaches to Study Somatic Transposition in Drosophila Using Whole-Genome DNA Sequencing	---	Somatic transposition, WGS, long-read sequencing, short-read sequencing	---	van den Beek et al., 2022	Drosophila	2022
Precise and Scarless Insertion of Transposable Elements by Cas9-Mediated Genome Engineering	---	CRISPR-Cas9, Knock-in, Homology-directed repair	LINE-1	Marie Weber et al., 2022	mammal	2022
Epigenetic Manipulation of Transposable and Repetitive Elements	---	Transcriptional repression/activation, TALE technology, Epigenetic modifications, Dual luciferase assay	LINE-1	Jachowicz 2022	mammal	2022
Genetic Knockout of TE Insertions by CRISPR-Cas9	---	CRISPR-Cas9, Knockout	---	Simpson and Chuong 2022	mammalian cell-lines	2022
Targeted analysis of transposable element methylation levels and transcriptome in single cells	scTEM-seq	Methylation, Trabscriptomics, Single Cell	---	Hunt et al., 2022	human cell-lines	2022

¶ Description

¶ Bioinformatic Protocols

¶ Molecular Biology Protocols