Computational protocol: Novel Essential Role of Ethanol Oxidation Genes at Low Temperature Revealed by Transcriptome Analysis in the Antarctic Bacterium Pseudomonas extremaustralis

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Protocol publication

[…] The data were de-multiplexed by Beckman Coulter Genomics. Reads alignment in P. extremaustralis genome and transcript abundance levels were quantified using the reads per kilobase per million mapped reads (RPKM) with Rockhopper software [], using default parameters. Concordance between replicates at 8°C and 30°C was verified by performing a Spearman correlation analysis of normalized counts (). Transcripts with less than 20 normalized reads were discarded from further analysis. Differential gene expression was considered as significant only when P<0.05 and Q<0.05 using Rockhopper software analysis. Functional enrichment of differentially expressed genes was determined using Blast2GO software by assigning the GO category to all genome sequences and to the differentially expressed genes []. […]

Pipeline specifications

Software tools Rockhopper, Blast2GO
Application RNA-seq analysis
Diseases Pelger-Huet Anomaly
Chemicals Acetaldehyde, Ethanol, Amino Acids, PQQ Cofactor, Polyhydroxyalkanoates