MOESM5 of Comparative analysis on the expression of L1 loci using various RNA-Seq preparations

Additional file 5. Manually curated set of L1 s with uniquely mapped non-strand-specific reads in 22Rv1 stranded in whole cell RNA-seq data from replicate 1. L1 s curated to be authentically expressed were labeled with a green color and L1 s curated to be rejected as passively expressed were labeled with a red color and its reason for rejection or acceptance was noted in the most right column following the guidelines for manual curation. In purple are examples of L1 s with antisense promoter activity. As the orientation of reads can not be distinguished in non-stranded data these L1 loci were curated to be not expressed off their own promoter and represent false negative calls. In blue are L1 loci that were curated to be authentically expressed in non-stranded data, but in fact had antisense reads mapped to it. These were considered false positive calls.