GSM2102000: G.m. anodic 1; Geobacter metallireducens; RNA-Seq
RNA was extracted individually from the triplicates of four experimental BES set-ups, which were inoculated either with pure cultures of Shewanella oneidensis MR-1, Geobacter sulfurreducens PCA, Geobacter metallireducens GS-15 or a mixed culture of the three strains. Prior to the extraction, all anodes with a biofilm were additionally pre-incubated in 3 ml of Bacteria Protect solution for 10 minutes at room temperature (Qiagen RNeasy Mini kit, Hilden, Germany). Total RNA was isolated from the anode-biofilms using the RNeasy kit provided by Qiagen according to the manufacturer’s instructions. Residual DNA was removed with an overnight DNase I digestion at 37°C. Further purification of RNA from DNA was conducted using the Ambion DNA-free kit (Life Technologies, Carlsbad, CA, USA). Aliquots from treated samples were subjected to PCR amplification with specific primers (Table 1) to validate the absence of genomic DNA. The Ambion MICROBExpress bacterial mRNA enrichment kit (Life Technologies) was used for rRNA depletion. Strand specific cDNA libraries were prepared from 50 ng of rRNA-depleted RNA following the TruSeq v2 RNA protocol (Illumina). The libraries were prepared using multiplex primers to allow simultaneous sequencing on a single lane, which was performed on a HiSeq1500 using SBS v3 kits (Illumina) generating paired end reads of 2 x 51 nt (G. sulfurreducens and S. oneidensis) or 2 x 100 nt (mixed species and G. metallireducens samples).
GEO
GSM2102000