NHE Jan 26 Notes

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Nick Elder

Group 2 intestines

In summary paper

  • include both fastQC rounds (trimmed 4 bases)
  • include papers we have read
  • research plan

RSem is the program to correlate the RNA seqs with annotated genome

Paper: Rapid changes in gene expression....

  • listed specifici genes
  • looked at early changes
  • WNT pathway
  • up regulation of growth and death factors
  • at 6hr time point, the cascade is in full force
    • at 30min, we want to identify which genes start the cascade
  • still selling the idea that the python is the best model for studying GI genetic regulation and morphology
  • do we have the same volume of reads?
  • took RNA from both the mucosa and serosa of the small intestine.
    • claimed that they didn't find significant difference in volume of sequncing between mucosa and cross section
    • mucosa changes the most morphologically
      • because mucosa is where most of the 'action' happens, comparing it to a cross section doesn't seem to distinguish it from the serosa
      • what about the serosa? huh?
      • Figure 1. did they really do anything different from sampling the same tissue multiple times?
        • Figure 1 C. same tissues from two animals are more different than the mucosa vs cross section from the same animal.
        • We're skeptical...........
  • Blasted sequences to another reptile, chicken (phylogenically close-ish) and humans
  • Figure 2. - 11 groups (clusters) of genes that are differentially regulated
    • main point seems to be that the largest change in expression level happens within the first 6 hours.
    • pooled data for every time point
    • divided the genes into clusters by a correlation threshold value set by the researchers
  • Figure 3. - heat map of gene expression
    • 6hr mark has the most number of yellow bars, mostly in one individual
    • 3 colors on the scale that are difficult to distinguish with no quantitative scale
    • should have shown the 11 cluster slices
  • Figure 4 has nice genes
  • They only sequenced the anterior of the intestine
    • pooling all of our animals could obscure data that could be more significant if sampled from different parts of intestine