1 / 7

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

ross-norris
Download Presentation

Case study: Saccharomyces cerevisiae grown under two different conditions

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 Cufflinks Pick up the 100 most highly expressed genes in the yeastRNAseq

  3. Oryza group Progress: • Arjan: Developeda package toretrievegene sequences. • Claire: Correlationbetween GC content and gene expression. • Robert: Trimming, Lengthsorting, TopHat, Cufflinks, retrieving Top100, formatting pipeline. • Ruud: Correlation between exon/intron size and gene expression. Generate output table.

  4. Oryza group • Biological questions on the selected genes: • Correlation between exon/intron sizeand gene expression • Correlationbetween GC content and gene expression

  5. Oryza group Using conserved palindrome motif list in yeast: Look for proportion of G/C-only repeats in top 100 gene list? Look for repeats length in top 100 gene list?

  6. Oryza group ... compare results with profile of less expressed genes? ... comparedifferentlyexpressedgenes on bothgrowth conditions? ... GO annotation? Plot data on cytoscape?

  7. Oryza group Next week packages: • Arjan: Codonusage over Top100 genes. • Claire: Correlationbetweenconservedpalindromesequencesand gene expression. • Robert: GO-annotation package. • Ruud: retrieve Top100 gene information from NCBI.

More Related