RNA-Seq of Arabidopsis thaliana Col-0 mitochondria
Total RNA was extracted from four-weeks-old WT and dPPR-nad7-DYW #1 plants using Trizol according to the manufacturers instructions (Ambion). DNA contaminations were removed using the DNA-free DNA Removal Kit (ThermoFisher). RNA (10 g) was treated with RiboMinusTM Plant Kit (ThermoFisher) following the manufacturer's protocol. About 1 ng of RNA from each experiment were used for library generation with the NEBNext Ultra II RNA Library Prep Kit according to the manufacturer's instructions. The libraries were quality controlled by analysis on an Agilent 2000 Bioanalyzer with the Agilent High Sensitivity DNA Kit (Agilent Technologies, Germany) for fragment sizes of ca. 200500 bp. Deep sequencing (2x 80 bp, v3 chemistry) was performed on a MiSeq sequencer (Illumina, San Diego, CA, USA) at the Genomics Service Unit (LMU Biocenter) yielding 5.7 and 5.7 Mio (WT replicate 1 and 2, respectively), as well as 5.5 and 6.2 Mio (dPPR-nad7-DYW #1 replicate 1 and 2, respectively) primary paired reads.