Illumina HiSeq 4000 paired end sequencing; RNAseq of young adult C. elegans animals fed on three different bacterial diets, E. coli OP50, B. subtilis PXN21 and a mixture of both
RNAseq of young adult C. elegans animals fed on three different bacterial diets, E. coli OP50, B. subtilis PXN21 and a mixture of both
2000 young adult worms (approximately 50-55h after plating of the L1s) grown on E. coli OP50, B. subtilis PXN21 or a 1:1 mix of E. coli:B. subtilis, were collected and washed three times with M9 + 0.01% Triton X-100 buffer. Three independent biological replicates were used for each experimental condition. The pellet was resuspended in 400 µl of RNA Lysis buffer (Quick-RNA Microprep Kit, Zymo Research) and worms were mechanically disrupted as previously described and kept at -80 °C. Total RNA was extracted from the samples according to the manufacturer's instructions.  RNA samples were sent to Edinburgh Genomics for QC check and sequencing. Briefly, quality check of the samples was performed using Qubit with the broad range RNA kit (Thermo Fisher Scientific) and Tapestation 4200 with the RNA Screentape for eukaryotic RNA analysis (Agilent). Libraries were prepared from 5 μg of total RNA using the TruSeq Stranded mRNA kit (Illumina), and then validated. Samples were pooled to create 9 multiplexed DNA libraries.
Experimental Factor: growth condition
mixed lawn (Escherichia coli OP50 and Bacillus subtilis PXN21)