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Case study: Saccharomyces cerevisiae grown under two different conditions

Oryza group Arjan , Claire, Robert & Ruud. Case study: Saccharomyces cerevisiae grown under two different conditions RNAseq data plataform: Illumina

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Case study: Saccharomyces cerevisiae grown under two different conditions

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  1. Oryza group Arjan, Claire, Robert & Ruud Case study: Saccharomyces cerevisiae grown under two different conditions RNAseq data plataform: Illumina Goal: Generate a platform where the user will input files and directory names, make the choice for trimmed or untrimmed RNAseq data to be assembled, and retrieve the top 100 expressed genes provided with biological information. Bioinformatics tools aimed to be used: TopHat, samtools, cufflinks, perl scripts, cytoscape (?)

  2. Oryza group RNAseq data Trimmed Untrimmed TopHat

  3. Oryza group TopHat Use Samtools to check coverage of mapped genome (Considerable difference between trimmed and untrimmed sequences?) Cufflinks

  4. Oryza group Cufflinks Pick up the 100 most highly expressed genes in the yeastRNAseq (Robert) • Biological questions on the selected genes: • Correlation between exon/intron sizeand gene expression (Ruud); • Develop a package toretrievegenessequences (Arjan); • Correlationbetween GC content and gene expression (Claire) ... compare results with profile of less expressed genes? ... comparedifferentlyexpressedgenes on bothgrowth conditions? ... GO annotation? Plot data on cytoscape?

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