title: GSM3703945: Bacteria_rG4seq_P_Li_rep1; Pseudomonas aeruginosa PAO1; RNA-Seq
library_construction_protocol: To examine the effect of rG4 sites on the transcriptome of P. auruginosa, 2 ml of mid-log-phase (OD600= 0.6) bacterial LB (Luria-Bertani) cultures (P. auruginosa PAO1strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the Ribo-ZeroTM rRNA Removal Kit (Bacteria) (Epicentre), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial rG4-seq reads were mapped to the P. auruginosa PAO1 (NC_002516.2) genome by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses.  GO enrich-ment analyses were conducted on all differentially transcribed genes using DAVID before data sets were imported into Cytoscape with an Enrichment Map plugin. The each sample inrG4-seq assay was repeated twice. TruSeq RNA sample prep kit protocol (Illumina)