RNA-Seq of Caulobacter crescentus SP3811; oxyR mutant; mid log phase; treated with 60 uM hydrogen peroxide for 15 minutes; biological replicate B
Caulobacter crescentus strain SP3811 (hydrogen peroxide-inducible genes activator mutant constructed from NA1000 strain; oxyR mutant) was grown aerobically at 30C in minimal medium (M2) until reach mid-log phase (OD600nm 0.5), and then was treated with 60 uM hydrogen peroxide for 15 minutes. Total RNA was extracted from 1 mL cultures using Qiagen RNeasy Plus Mini Kit (Qiagen) in accordance with the manufacturer's instructions. RNA concentration was determined by spectrophotometric ratio (O.D.260/280) and RNA integrity was verified by gel electrophoresis in 1% agarose. RNA samples were then submitted to the removal of ribosomal RNA using Ribo-Zero Magnetic Kit (Illumina) and the percentage of rRNA present was checked by running RNA 6000 Pico Kit using Agilent 2100 Bioanalyzer (Agilent). Complementary DNA was generated according to instructions of TruSeq RNA Sample Prep Kit v2 (Illumina). The sizes of cDNA libraries were verified using DNA 1000 Kit (Agilent) and were further normalized to 4 nM using Kapa Biosystems kit (Kapa Biosystems) for library quantitation prior to cluster generation. The samples were sequenced using MiSeq Reagent Kit v3 (Illumina) in accordance with the manufacturer's instructions. This is the biological replicate B. One may use the following sequences in order to trim the adapters from FASTQ files: Read 1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Read 2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT