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# euL1db data version 1.00
# Date : 05-10-14
# Methods Table
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#Name	Type	Approach	Starting_material	Throughput	Original_reference_PMID	Description	Link
RC-seq	enrichment	capture by hybridization followed by paired-end sequencing	genomic DNA	high	22037309	Sheared genomic DNA is hybridized to custom tiling arrays or to liquid-phase sequence capture probes targeting various families of retrotransposons. Captured DNA fragments are paired-end sequenced.	.
Fosmid sequencing	library screening	southern-blot followed by Sanger sequencing	fosmid	medium	20602998	40kb fosmid libraries showing evidences of structural variation are screened by Southern-blotting with an L1 probe and positive fosmids are Sanger sequenced.	.
Complete Genomics	computational	discordant read pairs identification	whole-genome paired-end sequence data	high	24389010	.	.
L1-seq	enrichment	ligation-mediated PCR followed by single-end sequencing	genomic DNA	high	20603005	Genomic regions downstream of L1 insertions are enriched by a ligation-mediated PCR approach using an L1HS-Ta specific primer which anneals in the 3' region of L1HS elements. The PCR products are then sequenced (single end reads).	.
Ewing PCR	enrichment	hemi-specific PCR followed by single-end sequencing	genomic DNA	high	20488934	Genomic regions downstream of L1 insertions are enriched by multiple rounds of primer extension. Priming is achieved with a specific primer which anneals in the 3' region of L1HS elements. These extension products are then amplified by a nested hemi-specific PCR using (i) an L1-specific primer and a degenerate oligonucleotide with a non-matching tail; (ii) a nested L1-specific primer and a tail-specific primer. This is followed by deep-sequencing (single end reads).	.
TranspoSeq	computational	discordant read pairs identification	whole-genome paired-end sequence data	high	24823667	.	http://www.broadinstitute.org/cancer/cga/transposeq
TranspoSeq-exome	computational	discordant read pairs identification	whole-exome paired-end	high	24823667	.	http://www.broadinstitute.org/cancer/cga/node/139
Ewing pipeline	computational	discordant read pairs identification	whole-genome paired-end sequence data	high	20980553	.	http://genome.cshlp.org/content/suppl/2010/05/18/gr.106419.110.DC1/supplemental_pipeline.tar.gz
Tea	computational	discordant read pairs identification	whole-genome paired-end sequence data	high	22745252	.	http://compbio.med.harvard.edu/Tea/
TraFic	computational	discordant read pairs identification	whole-genome paired-end sequence data	high	25082706	.	.
Candidate gene	enrichment	targeted PCR followed by Sanger sequencing	genomic DNA	low	.	.	.
Spanner	computational	discordant read pairs and split read identification	whole-genome paired-end sequence data	high	21876680	.	https://github.com/chipstewart/Spanner
ATLAS-seq	enrichment	anchored PCR followed by single-end sequencing	genomic DNA	high	.	.	.
Tangram	computational	discordant read pairs and split read identification	whole-genome paired-end sequence data	high	25228379	.	https://github.com/jiantao/Tangram
RetroSeq	computational	discordant read pairs identification	whole-genome paired-end sequence data	high	23233656	.	https://github.com/tk2/RetroSeq
VariationHunter	computational	discordant read pairs identification	whole-genome paired-end sequence data	high	20529927	.	http://compbio.cs.sfu.ca/strvar.htm