title: GSM2991338: CK-1; Pseudomonas aeruginosa PAO1; RNA-Seq
library_construction_protocol: To examine the effect of RpoN on the transcriptome, 2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PAO1 and ∆rpoN strains) 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 MICROBExpress kit (Ambion), 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 RNA-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0). 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 in RNA-seq assay was repeated twice. TruSeq RNA sample prep kit protocol (Illumina)
attributes.tag: GEO Accession
attributes.value: GSM2991338