Resources from the Burns Lab

Transposon Insertion Profiling (TIP)seq protocols
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. doi: 10.1186/s13100-019-0148-5.

Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells.
McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, Liu C.
Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190335. doi: 10.1098/rstb.2019.0335. 

For TIPseqHunter analysis, see: 
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.
And software, https://github.com/FenyoLab/TIPseqHunter 

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).

A detailed protocol for using this reagent in immunohistochemistry experiments can be found here:
Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues.
Sharma R, Rodić N, Burns KH, Taylor MS.
Methods Mol Biol. 2016;1400:261-80.

ORF2p antibodies
ORF2p antibodies are currently being prepared for commercial production by Abcam. In the meantime, our lab has limited ability to distribute these reagents. Investigators are welcome to contact us for updates.

Reference:
LINE-1 ORF2p expression is nearly imperceptible in human cancers. 
Ardeljan D, Wang X, Oghbaie M, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D, Burns KH, LaCava J. 
Mob DNA. 2019 Dec 31;11:1. doi: 10.1186/s13100-019-0191-2.

Plasmids
Our lab has deposited LINE-1 expression plasmids at Addgene.

Reference: 
Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication.
Ardeljan D, Steranka JP, Liu C, Li Z, Taylor MS, Payer LM, Gorbounov M, Sarnecki JS, Deshpande V, Hruban RH, Boeke JD, Fenyö D, Wu PH, Smogorzewska A, Holland AJ, Burns KH.
Nat Struct Mol Biol. 2020 Feb;27(2):168-178. 

Software for Quantifying Interspersed Repeat Expression (SQuIRE)
Our lab has developed a computational approach for evaluating interspersed repeat expression in RNAseq data. This can be used to identify L1, ERV, and Alu expression that may be involved in viral mimicry.

Reference:
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. doi: 10.1093/nar/gky1301.

Code is available, https://github.com/wyang17/SQuIRE