STRIPE-seq of SS3
Whole RNA extracted from mid log S. cerevisiae cells were DNase(I)d followed by rRNA depletion similar to TSS-Seq. Libraries were then prepared following STRIPE-seq protocol by Policastro et al, 2020 with our modifications: 9-base UMI was used; 10-mer RTO was used; dual indexing logos were added in the final step of library amplification. Amplified libraries were initially purified with SPRI select beads to remove small fragments and then gel extracted from 1.8 % agarose gel to size select library smears from 200-800 bp using NucleoSpin Gel and PCR Clean-up (Macherey Nagel, NC0389463) kit. Thus, generated dual indexed STRIPE-seq libraries which were sequenced together with TSS-seq libraries. TSS-seq and STRIPE-seq libraries were pooled and sequenced on an Illumina NovaSeq-S1-200 cycles sequencing flowcell  using custom primer.