RNA-Seq of Caulobacter crescentus NA1000; wildtype; mid-log phase; treated with 100 uM 2,2-dipyridyl for 2h; biological replicate B
Caulobacter crescentus strain NA1000 was grown aerobically at 30 C in minimal medium (M2) until reach mid-log phase (OD600 0.5), and then was treated with 100 uM 2,2-dipyridyl (Sigma) for 2 hours. Total RNA was extracted using Qiagen RNeasy Plus Mini Kit (Qiagen) in accordance with the manufacturer's instructions. RNA samples were then submitted to the removal of ribosomal RNA using Ribo-Zero Magnetic Kit (Illumina). The quality of the isolated RNA and the percentage of rRNA present were 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 cDNA libraries were further normalized to 4 nM using the 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