Monthly Archives: February 2016

DNA quantitation and quality check

Today I determined DNA yield for several samples that I had not yet tested with the Qubit. Here are the results (along with previous Nanodrop results), which can also be found in this spreadsheet:

Sample # Nanodrop DNA conc. (ng/ul) Qubit conc. (ng/ul) Sample volume Total DNA yield (ng)
past_100 7.36 2.28 200 456
past_1 19.06 11.3 200 2260
past_10 36.59 20 200 4000
past_97 7.56 too low 200
past_w11 179.65 35.2 50 1760
past_3 120.01 36.6 50 1830
past_2 223.21 99.4 50 4970
past_w1 437.86 330 50 16500
past_4 198.65 47.2 50 2360
past_w3 331.75 172 50 8600
past_5 193.93 77 50 3850
past_6 212.31 66.2 50 3310
past_7 229.16 27.4 50 1370
past_9 343.89 244 50 12200
past_8 106.39 37.6 50 1880
past_12 209.58 18.2 50 910


I also evaluated DNA quality on a gel for several samples. Here is the gel:


As can be seen here, some samples look pretty good, some look ok, and some look like crap. Why such a range? I have no idea, they were all preserved and extracted the same way. Past95 and past19 in particular are particularly bad. These samples should be re-extracted.

DNA extraction

Today I completed the final round of DNA extractions from my Belize Porites samples collected in November using the Qiagen DNeasy Blood and Tissue kit. Based on my experience in previous extraction efforts (see previous post), I was generous with tissue quantity. And again, in many cases the tissue was so loosely attached to the skeleton that it was easy to either scoop or scrape off with little skeletal material. As before, I used a single elution volume of 50 ul, which was passed though the column twice. I only evaluated yield this time on the Nanodrop. All samples were in the range of 100 – 400 ng/ul. Based on comparative Qubit results from last time, these Nanodrop values may overestimate yield by approximately double. Also note that most samples had significant absorbance around 230 nm, suggesting the presence of salts, carbohydrates, or phenolic compounds.

Note here that some of the samples in this batch were Porites porites (ppor) as opposed to Porites astreoides (past). Also included in this batch were three samples collected from the top, middle, and bottom of a single P. astreoides colony (w, for within).

Here is the Nanodrop report:




I also ran these samples on a gel. I followed this gel protocol with one modification: I used 1 ul of all samples mixed with 4 ul AE buffer and 1 ul loading dye. There appears to be high molecular weight DNA in all visible samples.


DNA extraction

I have been moving forward with extraction of DNA from P. astreoides samples using the Qiagen DNeasy kit. On Monday/Tuesday I did 16 samples, then another 10 samples (actually 9; one was divided in two). For the first set of 16, I did an overnight lysis (6pm to 9am) with no homogenization. Most of the tissue was very loose and easily scraped off the skeleton or scooped from the bottom of the tube. My initial results (see previous post) suggested that larger quantities of tissue were more successful, so I was fairly generous with tissue quantity. I did two 200 ul elutions into two separate tubes. I measured DNA quantity in the first elution with the Qubit HS assay. Here are the results (again, for the first elution only):

Sample # Qubit conc. (ng/ul) Sample volume Total DNA quantity (ng)
15 5.92 200 1184
16 3.46 200 692
96 6.82 200 1364
19 5.4 200 1080
14 3.92 200 784
82 7.38 200 1476
98 7.92 200 1584
13 10.4 200 2080
12 3.1 200 620
18 5.88 200 1176
99 5.16 200 1032
17 10 200 2000
95 5.88 200 1176
11 10.4 200 2080
80 10.8 200 2160
81 8.82 200 1764


For the next set of 10 samples, I did a few things differently. Again, I tried to be generous with tissue quantity. For a few samples, the tissue volume of the pellet was nearly 100 ul. I ranked the tissue quantity on a scale of 1 to 10, 1 being the lowest. I also ranked the sample color after the lysis period to get a second qualitative measure of tissue quantity. I homogenized three of the most dense samples lightly with a plastic pestle (86, 90, 83). The lysis period was from 4:30pm to 9:30am. The lysis did not appear complete, so for the last hour of lysis, I added an additional 180 ul of buffer and 40 ul of proteinase K, and disrupted a few of the most dense samples by pipetting. Sam suggested elution with 50 ul instead of 200 ul, and reusing the original eluate for the second elution. I quantitated the DNA with both Nanodrop and Qubit for comparison. Here are the results:


Sample # Tissue quantity rank (1 = low) Color rank after lysis Nanodrop DNA conc. (ng/ul) Qubit conc. (ng/ul) Sample volume Total DNA quantity (ng)
87 1 1 166.2 45.6 50 2280
89 2 3 122.9 48 50 2400
85 3 4 313.9 143 50 7150
88b 4 2 214.2 121 50 6050
84 5 6 398.1 188 50 9400
91 6 9 329.7 194 50 9700
88a 7 5 292.6 182 50 9100
86 8 7 359.4 234 50 11700
90 9 8 312.3 218 50 10900
83 10 10 377.7 194 50 9700

The Nanodrop quantity estimates were approximately double those from the Qubit. Qubit values were used for estimation of total yield in the last column. Also, from my qualitative estimate of tissue quantity, it appears that higher quantities tended to be better. If you plot the data, there appears to be an asymptote, so I may have reached optimum tissue quantities.



DNA extraction trial run #2

Yesterday I did a second trial run with the same P. astreoides samples used in the previous run (sample #s 1, 10, 97, 100; see previous post). This time, however, I used the Qiagen DNeasy Blood and Tissue Kit. I used approximately the same amount of tissue used in the previous runs, perhaps slightly more. All tissue samples were largely detached (sloughed off) from the skeleton as before, so for most samples I simply scooped loose tissue from the tubes. I did not do any homogenization. However, I did rinse the tissues three times in PBS, compared to only once in the previous run with the EZNA Mollusc Kit. Another thing that I did differently was a shorter 2.5 hr lysis at 56ºC, instead of a 24 hr lysis at 37ºC with the mollusc kit. I chose this lysis duration mainly out of convenience since I was unable to come back the following day. I also vortexed the samples periodically during lysis. At the end of the lysis period, I noted the following with respect to the appearance of the samples: samples 1 and 10, no visible skeletal material, some bits of intact tissue; sample 97, some skeletal material present, very little visible tissue; sample 100, no skeletal material, many small bits of tissue. So from these I estimated that the only sample that was fully lysed was #97. However, I think this was also the sample with the least amount of tissue.

The good news is that this time there was significantly more DNA in most of the samples. Here is the nanodrop report (the second half of the samples with a -2 are the second elution).



My sense is that sample 97 had low DNA concentration due to a low tissue quantity. As for sample 100, I think there may have been too much tissue and incomplete lysis. But I would not say there was huge variance in the amount of sample used, so the large differences in DNA quantity are a bit perplexing. In any case, the results are encouraging and I will move forward with DNeasy for all samples, perhaps with a longer lysis duration and some light homogenization.