Marchantia polymorpha chloroplast, differential RNA-seq

Differential RNA-seq of Marchantia polymorpha chloroplasts to map transcription start sites across the chloroplast genome.Two RNA samples were isolated from Marchantia polymorpha chloroplasts. The samples were each split in two halves. One half was treated with Terminator 5' phosphate dependent exonuclease (TEX) in order to selectively degrade RNAs with 5' monophosphate termini, while primary transcripts with 5' triphosphate termini are resistant to degradation. After cDNA synthesis, the TEX sample will be enriched in primary transcript derived sequences relative to the control . Following sequencing and mapping, transcription start sites can be identified by comparing coverage in the TEX treated libraries against the controls.