Schematic of experiments for obtaining mRNA pools enriched in SL1- or SL2-spliced variants of all expressed genes. Three pools of poly-adenylated RNA were isolated from total RNA: total polyA mRNA, a SL1-spliced mRNA fraction, and a SL2-spliced mRNA fraction. Briefly, biotinylated oligo-dT probes were used to purify the entire polyA-mRNA from total RNA. The mRNA was split into three aliquots, where one of the aliquot was directly used for RNA-seq, while the SL1-spliced or SL2-spliced mRNA was isolated from the remaining two aliquots, using biotinylated oligo probes with sequences complementary to the respective splice leaders. Streptavidin-coated magnetic beads were used to pull down the biotinylated probes.
