Computational protocol: Ecological interactions among Saccharomyces cerevisiae strains: insight into the dominance phenomenon

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Protocol publication

[…] An Illumina RNA amplification kit (Thermo-Fisher) was used in order to amplify the small amount of RNA extracted from the cells separated by means of cytometry. Sequencing was performed by means of the 5500 SOLiD system (Life Technologies, Madrid, Spain). Seventy-eight million reads per strain were obtained, and short sequences (75 bp) were assembled and aligned using a reference S. cerevisiae strain (Saccer2). The values of FPKM (Fragments Per Kilobase of exon per Million fragments mapped) were transformed for the statistical test as log2 (FPKM1/FPKM2) and uploaded on Cuffdiff (Cufflinks V1.3.0, http://cufflinks.cbcb.umd.edu/), where FPKM1 stands for the dominant strain data and FPKM2 stands for the non-dominant strain data. The FPKM parameter was used for pair end RNA-Seq experiments, where fragments were sequenced from both ends, and two reads were performed for each fragment. The Q value, which represents the significance value of the statistical analysis, performed through the use of a cufflink platform, was calculated, and significant transcriptome differences were identified. A functional analysis was performed to search for any significantly overrepresented gene ontologies (GO) in a set of genes, using the Genemania functional network predictive online tool. […]

Pipeline specifications

Software tools Cufflinks, GeneMANIA
Application RNA-seq analysis
Organisms Saccharomyces cerevisiae