DNA Methylation Quantification – Coral DNA from Jose M. Eirin-Lopez (Florida International University)

Ran the coral DNA I quantified on 20160630 through the MethylFlash Methylated DNA Quantification Kit [Colorimetric] (Epigentek) kit to quantify global methylation.

Used 100ng of DNA per 8uL per replicate (x2 replicates = total 200ng in 16uL). Calcs are here (Google Sheet): 20160705_coral_DNA_methylation_calcs

Manufacturer’s protocol was followed.

Dilutions of kit reagents:

ME5 (1:1000) 2.6uL ME5 + 2597.4uL diluted ME1

ME6 (1:2000) 1.3uL ME6 + 2598.7uL diluted ME1

ME7 (1:5000) 0.52uL ME7 + 2599.48uL diluted ME1

Samples were quantified on the Seeb’s plate reader @ 450nm  (Wallac 1420 Victor 2  [Perkin Elmer])


Google Sheet: 20160707_coral_DNA_methylflash

sample treatment 5-mC(ng)
H1_1 nitrogen 0.8712248853
H1_10 nitrogen 0.6917168368
H1_12 control 0.2738478893
H1_5 nitrogen & phosphorous 0.9663585942
H1_6 control 0.6494783825
H1_8 nitrogen & phosphorous 0.4244913398
H24_1 nitrogen 0.372603297
H24_10 nitrogen 0.4237237786
H24_12 control 0.5350511937
H24_5 nitrogen & phosphorous 0.1495527697
H24_6 control 0.2291900804
H24_8 nitrogen & phosphorous 0.2213437801
H5_1 nitrogen -0.1233169902
H5_10 nitrogen 0.6997668774
H5_12 control 0.2307000493
H5_5 nitrogen & phosphorous -0.07790933048
H5_6 control 0.4562401662
H5_8 nitrogen & phosphorous 0.5949647121


Overall, it’s difficult to really interpret these results. I believe the data is a time course (e.g. H5 = hour 5, H24 = hour 24). Additionally, looking at treatments, there appear to be replicates, but it’s not clear what type of replicates they are (i.e. technical or biological). Generally, it seems like the control samples have lower quantities of methylated DNA than the treated samples. However, this doesn’t hold true for all three of the groups.

And, not that it really matters, but I don’t even know what species this is…

In any case, this was an attempt to gather some preliminary data for a grant that Steven is attempting to put together, so the original experiment and the subsequent data aren’t as robust as one would expect for a full-blown research project.

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