JP Jan 26 16
RSem = program to correlate the RNA data seqs with associated genome. What information can we use from the fastQC data before and after removing bar codes?
Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding 2015
Reading notes:
This paper gave us a lot of specific genes, activated around 6-12 hours.
"The WNT signaling pathway likely plays a role in growth and maintenance of the small intestine upon feeding, with multiple genes within this cascade experiencing significant differential expression throughout the digestion process" (152).
Found controlled activation and execution of apoptosis (Fig 4A)
Table 1: Separated cross sectional and mucosa from intestinal tissue. Mucosa changes mass the most. Figure 1: They argue that the mucosa is no different from the cross section. But, mucosal cells are in the cross section. There's mucosa in both samples. Higher range in the lower left corners because any little variance causes a larger spread when the scale is smaller (between 1 and 10). They're saying (Fig1C) that two of the same tissue samples in different individuals are less similar than the two types of tissues from the same individual. Two animals are not the same. Are two animals more different than each other than two tissues are? Unconvincing.
Subject to interpretation on whether they just sampled the same tissue twice.
Annotated python genes using lizard, human, and chicken homologies. Restrictive.
Figure 2: gene clusters. Does give a y axis for expression change. Shows significant changes in the first 6 hours. Cluster of 11 determined by investigator - how much correlation they want to see before "cutting the tree"; software clusters into so many groups, the number of which is determined by the investigator.
Figure 3: the left tree represents correlation in expression. Rows are genes, columns are snakes, separated by time. Low-high scale is a little vague, no quantitative value; things squished into the same scale regardless of expression (want to see logarithmic or something). Would have been nice to see the 11 clusters visualized as separated.
- Figure 4 has good information for us to investigate
- "Combined with data previously published (10), new data are accessioned in the National Center for Biotechnology Information Short Read Archive (SRP051827)" (p. 149).
- Difficulty in our experiment with comparing to published results / clustering within our own data, as we don't know what part of the intestine we got.
Performed a trim; trim the first 4 bases, remove bases with phred score <30.
The duplication levels have not gone down. Per base sequence content has gone down.
New overrepresented sequences will be worth analyzing. Kmer content changed before and after trim. We need to analyzed what this is. How frequent does a string of 7 bases exist?
