13 June 2014
ddRADseq and presentationNext post Previous post
Qubit for DNA extracions before and after double-digest
Waiting on Bioanalyzer results to confirm digestion and then will anneal adapters
Modified “expression type” categories to include:
Under this scheme, 57% of High transcripts are PositiveLinear while 72% of Low transcripts are NegativeLinear. This is consistent with the motivating observation that many of the Low transcripts appear to gradually decrease, compared to the High transcripts that were up-regulated at high temperatures.
Samples 1-5 (4e, 8e, 12e, 16e, 20e) are the raw DNA from the extraction. All look good and large.
Samples 6-11 (1d, 4d, 8d, 12d, 16d, 20d) are the double digested DNA. Shape looks different then before when it was smooth. Something wrong with the digestion? Or must higher input DNA quantity so see more DNA? But why only at the small size distribution?
To test if the digestion worked leaving sticky ends, SHC performed annealing reaction. Expect to see shift if distribution of 76 bp if adapters anneal correctly.
Parsing responsive transcripts into categories - mismatch between the “type” and plots. Tracked this bug down to the fact that I (correctly) assigned expression type from the simplified models after AIC but was plotting from the model including only temperature.
More generally - does it make sense biologically to partition the High genes into PositiveLinear and HighOn?
Discussed this with NG. Two issues:
Working on presentation for Evolution.
Using Beamer as I need PPT of PDF format and I couldn’t figure out how to get reveal.js HTML presentation to PDF.
Digested DNA with annealed adapters. From Wednesday’s results, expected to see shift up of 76 bp. Problem is that the high concentration of adapters (36 bp) swamp the DNA. Potential problem that there’s a large peak at about 76 bp which would be an adapter dimer.
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