title: Dual RNA-seq of caeca cells dissected from aposymbiotic S. oryzae fed on grain
design: Total RNA was extracted using the Picopure RNA Isolation kit (Thermo Scientific). Total RNA was eluted in an 11 l elution buffer and RNA quality and quantity were assessed using an AgilentAglient 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) with an RNA6000 Pico Lab Chip. For each cell type, three replicates (pool of one to four caps) were analysed. RNA samples of 4-15.8 ng of the total RNA were subjected to dual RNA-Seq library construction, using the Ovation Solo Universal RNA-seq protocol (Tecan, Switzerland). Depletion of rRNA was performed with a total of 170 rRNA depletion probes designed for S. oryzae (5.8S, 18S, 28S and mitochondrial 12S and 16S) S. pierantonius rRNA sequences (5S, 16S and 23S) using the Ovation Solo Universal RNA-seq protocol (Tecan, Switzerland), according to the manufacturers instructions. Paired-end reads of 75 nucleotides were obtained using an Illumina NextSeq 500 instrument (Illumina) at the sequencing platform of the Institut de Gnomique Fonctionnelle de Lyon, Ecole Normale Suprieure de Lyon, France.