RNA-seq of MCF-7 (breast adenocarcinoma) and 2102Ep (embryonic carcinoma) cells upon LINE-1 knockdown.. RNA-seq of MCF-7 (breast adenocarcinoma) and 2102Ep (embryonic carcinoma) cells upon LINE-1 knockdown.

To measure the levels of expression of retrotransposon individual copies, and particularly of LINE-1 (L1) elements of the L1HS-Ta subfamily, we performed 2x150 bp paired-end and strand-specific RNA-seq on polyA+ RNA of MCF-7 and 2102Ep cells, which express high levels of L1. To confirm the origin of the L1-specific signal, we also performed RNA-seq upon shRNA-mediated L1 knockdown. sh960 relates to a scramble shRNA control. sh1083 and sh1085 relate to two distinct shRNAs directed against the ORF1 region of L1.3 (GenBank L19088) as a prototype L1HS-Ta.