TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline

The TE-Seq pipeline conducts an end-to-end analysis of RNA sequencing data, examining both genes and TEs. It implements the most current computational methods tailor-made for TEs, and produces a comprehensive analysis of TE expression at both the level of the individual element and at the TE clade level. Furthermore, if supplied with long-read DNA sequencing data, it is able to assess TE expression from non-reference (polymorphic) loci. As a demonstration, we analyzed proliferating, early senescent, and late senescent lung fibroblast RNA-Seq data, and created a custom reference genome and annotations for this cell strain using Nanopore sequencing data. We found that several retrotransposable element (RTE) clades were upregulated in senescence, which included non-reference, intact, and potentially active elements. We applied our pipeline to RNA-Seq data from our laboratory on LF1 cells spanning three biological conditions: LF1 cells were passaged to replicative senescence, and were harvested 4 and 16 weeks later, yielding early senescence (ESEN) and late senescence (LSEN) conditions. Early passage proliferating LF1 cells (PRO) were used as a control. Poly-A selected, stranded, 150bp paired-end libraries were sequenced in quadruplicate.