Resources from the Burns Lab

Antibodies to detect LINE-1-encoded proteins
ORF1p antibodies
We developed a mouse monoclonal antibody, 4H1, that recognizes epitope MENDFDELRE on human LINE-1 ORF1p. 
​The reagent can be purchased from Millipore Sigma (catalog no. MABC1152).

ORF2p antibodies
We developed a rabbit monoclonal antibody, MT49, that recognizes epitope DRSTRQ in the EN domain of ORF2p. 
The reagent can be purchased from Abcam (catalog no. ab263435). 

Plasmids
Our lab deposits plasmids at Addgene for distribution to other labs.

Transposon mapping methods
These two manuscripts detail our protocol for amplifying LINE-1 insertions sites in the human genome:

Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome.
Steranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH. Mob DNA. 2019 Mar 8;10:8. 

Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. 
Tang Z, Steranka JP, Ma S, Grivainis M, Rodić N, Huang CR, Shih IM, Wang TL, Boeke JD, Fenyö D, Burns KH. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E733-E740.
Code is available, https://github.com/FenyoLab/TIPseqHunter 

RNAseq analysis
Our lab has developed a Software for Quantifying Interspersed Repeat Expression (SQuIRE) for evaluating transposable element expression in RNAseq data. 

SQuIRE reveals locus-specific regulation of interspersed repeat expression.
Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. Nucleic Acids Res. 2019 Mar 18;47(5):e27. 
Code is available, https://github.com/wyang17/SQuIRE