title: GSM9043340: tratamiento_rep3; Paracoccus denitrificans PD1222; RNA-Seq
library_construction_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. Genomic DNA contamination was removed by DNase I (RNase-free) treatment (Thermo Scientific). RNA concentration and purity were measured using a NanoDrop 200c spectrophotometer (Thermo Scientific), and RNA integrity was assessed with an Agilent 2100 Bioanalyzer. The resulting RNA samples were used for both RNA sequencing (RNA-seq) and reverse transcription quantitative PCR (RT-qPCR). RNA-Seq was performed using total RNA extracted from Paracoccus denitrificans PD1222 grown with and without applied constant potential. Ribosomal RNA was depleted using the Ribo-Zero Plus Microbiome Depletion Kit (Illumina). The remaining mRNA was chemically fragmented to ~150–200 bp, and cDNA libraries were synthesized using the Illumina Stranded Total RNA Prep Kit (Illumina). Libraries were quantified using the Qubit dsDNA HS Assay Kit and a Qubit v4 fluorometer (Thermo Scientific). Sequencing was carried out at the UUSMB (Unidad Universitaria de Secuenciación Masiva y Bioinformática, UNAM, México) on an Illumina NextSeq 500 platform using a 2 × 75-cycle sequencing kit (NextSeq 500/550 Mid Output Kit, 150 cycles). Differential expression analysis was performed using DESeq2 (Anders and Huber, 2010). Genes with adjusted p-value < 0.05 and fold change > 1 were considered significantly differentially expressed.