NHE Jan 26 Notes
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