Strand asymmetry in MPRA Signal. Strand asymmetry in MPRA Signal

We analyzed data from sequencing-based massively parallel reporter assays (MPRAs) retaining the strand orientation of the alignments. These analyses showed pervasive asymmetry in reporter signal from test element strand orientation. Present in elements derived from all regions of the human genome, we found test elements derived from gene bodies display concordant strand asymmetry with the sense orientation of the gene body. Furthermore, we observe that test elements form Alu sequence also present concordant strand asymmetry with Alu retrotransposon features. We establish sequence features that drive some of this asymmetry. Overall design: In one set of experiments, we created a STARR-seq library from several BACs encompassing a region near the HTT gene. We transfected these into four cell types: A549, BE(2)-C, HepG2, and K562 cells. We harvested both RNA and DNA and created sequencing libraries. We sequenced the sequencing libraries using an Illumina Next-seq. In another set of experiments, a STARR-seq library was created using BACs near the SORT1 gene. We transfected these into HepG2 cells. Again, we harvested RNA and DNA and created sequencing libraries. We sequenced these libraries on an Illumina Next-Seq