NHE Jan 26 Notes

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.