After RT, nuclei were pooled and redistributed into 96-well plates for indexed hairpin ligation. Then, they were pooled and split to final 96-well plates. After second-strand synthesis, nuclei were lysed, and the resulting lysates were split into two plates. One plate underwent Tn5 tagmentation and indexed PCR to generate a transcriptome library. The other plate was used for indexed enrichment PCR targeting the synHEK3 and shRNA transcripts.
