rr oct14 2011

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  1. 1. Analysis of ribo-seq data:which measure to use when analyzing your data?
    Reut Shalgi
    RR Oct 14 2011
  2. 2. Global transcriptomics & proteomics data from 3T3 cells
    Schwanhausser et al. Nature , May 2011
    SILAC time course: 1.5h, 4.5h, 13.5h
    prot. abundance (molec/cell)
    • prot. syn. rates (molecules/(mRNA*h))
    • 3. prot life (h)
    mRNA synthesis labeling (4sU) for 2 hrs:
    • mRNA abundance (molec/cell)
    • 4. transcription rates (molecules/(cell*h))
    • 5. mRNA halflives (h)
  3. Comparison with my 3T3 ribo-seq & RNA-seq data
    Selbach mRNA copy num correlate with my RPKM
    Selbach
    mRNA copy num vsprot copy num
    my fp density vs. my RPKM
  4. 6. Comparison with my 3T3 ribo-seq & RNA-seq data
    ANOTA TE
    classical TE
    My recommendation:
    • best to use fp density to describe your data
    • 7. dont use TEs, not sure what they represent