title: Transcriptome of Halomonas sp. MNB13 with or without manganese dioxide
design: After strain MNB13 was cultured to mid-log-phase, cells were collected by centrifugation (8,000  g for 10 min at 4 C) and then resuspended in basal medium with or without 0.5% MnO2, each repeated three times. After 48 h of incubation, cells were collected, washed three times with ice-cold 0.85% NaCl. Total RNA was extracted using Trizol (Rio et al., 2010). The quality of the extracted RNA was examined using Thermo NanoDrop One and Agilent 4200 Tape Station. Ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Epicentre, Illumina Inc). Libraries were constructed using the NEB Next Ultra  Directional RNA Library Prep Kit (Illumina, USA), and sequencing was performed in rapid mode with a read length of 150 nt (Illumina PE150, Illumina Inc., USA; Guangdong Magigene Biotechnology Co., Ltd., Guangzhou, China). Clean reads were obtained by removing sequences with overrepresented adaptors, short reads (< 75 nt), pair-end reads with > 5% "N" bases and reads with over 20% bases with quality less than 20. All clean reads were aligned to the genomic sequence of MNB13 using Bowtie2.