Computational protocol: Genome-wide transcriptome profiling of nitrogen fixation in Paenibacillus sp. WLY78

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Protocol publication

[…] Total RNA was isolated from Paenibacillus sp. WLY78 grown in N2-fixing and non-N2-fixing conditions, respectively. cDNA library construction and SOLiD sequencing from the total RNA were completed in Beijing Genomics Institute (Chinese Academy of Sciences) and three technical replicates of each sample were carried out. Raw sequencing reads were mapped against the Paenibacillus sp. WLY78 genome, using the programme BWA as previously described [, ]. We use DEGseq for identifying differentially expressed genes from RNA-seq data []. Transcript level differences with adjusted P values of <0.001 were considered to be significant. […]

Pipeline specifications

Software tools BWA, DEGseq
Application RNA-seq analysis
Organisms Paenibacillus polymyxa
Chemicals Nitrogen, Superoxides