Bioanalyzer dna 7500 dna chip

Depleted RNA was used for RNA-Seq library preparation with the Epicentre ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre-Illumina, CA) following the manufacturer’s protocol (EPILIT329 Rev. C). Agencount AMPure beads (Beckman Coulter, IN) were used to purify the cDNA, and unique indexes were added during 13 cycles of library amplification. The final RNA-Seq libraries were purified with Agencount AMPure beads (Beckman Coulter, IN) and quantified with a Qubit fluorometer (Life Technologies, CA). The library quality was assessed on a Bioanalyzer DNA 7500 DNA Chip (Agilent, CA), and samples were pooled and diluted. Two paired end sequencing runs were completed on an Illumina MiSeq Instrument (Illumina, CA) using the standard protocol. Raw sequencing fragment reads were mapped in CLC Genomics Workbench 9.0.1 (CLC bio, Denmark) using default prokaryote settings to genome [GenBank:CP000568.1] and the resulting unique gene read counts output was used for differential expression analysis with the R package DeSeq2 according to published methodology23 (link). RNA-Seq gene expression as well as raw sequencing and mapped reads data have been deposited in NCBI GEO accession number GSE87407.