NHE Jan 26 Notes - Revision history

Nielder at 19:21, 26 January 2016

2016-01-26T19:21:47Z

2016-01-26T19:02:30Z

2016-01-26T18:35:03Z

New page

[[Nick Elder]]

[[Group 2 intestines]]

← Older revision		Revision as of 19:21, 26 January 2016
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	***Figure 1. did they really do anything different from sampling the same tissue multiple times?		***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.		****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

← Older revision		Revision as of 19:02, 26 January 2016
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	[[Group 2 intestines]]		[[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.