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Friday, March 31, 2017

Numbers, Numbers, Numbers

“Having had the green light to run all protocols and using all four bacteria cultures I did exactly that and was left drained at the end of that day” – Thursday, March 23rd

This week was dedicated to analyzing the products of the DNA extraction methods using microvolume UV-Vis spectrophotometer technology. The results are on the tables below and can be overwhelming to look at.

There were four culture broths used, each with a different color cap:
-Green (g)
-White (w)
-Red (r)
-Blue (b).

There was a total of six protocols:
-Boiling (BP)
-TE Boiling (tBP)
-TE Freeze and Thaw (tFT)
-Lysis (L)
-Meat Tenderizer (MT)
-Commercial Kit (C)
Each culture was used to conduct all of the protocols to determine which protocol was the best. Given that there were four cultures, the experiment was conducted four different times technically. Here are the results:

Sample ID
Nucleic Acid
Unit
260/280
Sample Type
Factor
BPg(Blank)
BPg
33.7
ng/µl
1.48
DNA
50
BPg
33.3
ng/µl
1.48
DNA
50
BPg
34
ng/µl
1.49
DNA
50
BPg
34
ng/µl
1.49
DNA
50
BPg
33.7
ng/µl
1.49
DNA
50
BPw(Reblank)
BPw
31.2
ng/µl
1.52
DNA
50
BPw
30.5
ng/µl
1.49
DNA
50
BPw
35.5
ng/µl
1.4
DNA
50
BPw
30.8
ng/µl
1.49
DNA
50
BPw
31.9
ng/µl
1.52
DNA
50
BPr(Reblank)
BPr
77.2
ng/µl
1.57
DNA
50
BPr
76.7
ng/µl
1.56
DNA
50
BPr
77.2
ng/µl
1.57
DNA
50
BPr
76.7
ng/µl
1.57
DNA
50
BPr
80.2
ng/µl
1.57
DNA
50
PBb(Reblank)
BPb
56.6
ng/µl
1.6
DNA
50
BPb
57.7
ng/µl
1.59
DNA
50
BPb
59
ng/µl
1.61
DNA
50
BPb
57.8
ng/µl
1.58
DNA
50
BPb
57.4
ng/µl
1.61
DNA
50
Sample ID
Nucleic Acid
Unit
260/280
Sample Type
Factor
tBPg(Blank)
tBPg
885.5
ng/µl
1.43
DNA
50
tBPg
883.3
ng/µl
1.44
DNA
50
tBPg
968
ng/µl
1.43
DNA
50
tBPg
885
ng/µl
1.44
DNA
50
tBPg
873.8
ng/µl
1.44
DNA
50
tBPw(Reblank)
tBPw
933.8
ng/µl
1.5
DNA
50
tBPw
956.7
ng/µl
1.5
DNA
50
tBPw
949.1
ng/µl
1.5
DNA
50
tBPw
954.4
ng/µl
1.5
DNA
50
tBPw
948.2
ng/µl
1.49
DNA
50
tBPr(Reblank)
tBPr
963
ng/µl
1.56
DNA
50
tBPr
963.8
ng/µl
1.56
DNA
50
tBPr
967.9
ng/µl
1.56
DNA
50
tBPr
968.6
ng/µl
1.56
DNA
50
tBPr
971.5
ng/µl
1.55
DNA
50
tBPb(Reblank)
tBPb
977.2
ng/µl
1.58
DNA
50
tBPb
997.7
ng/µl
1.57
DNA
50
tBPb
987.7
ng/µl
1.57
DNA
50
tBPb
966.8
ng/µl
1.57
DNA
50
tBPb
993.3
ng/µl
1.57
DNA
50
Sample ID
Nucleic Acid
Unit
260/280
Sample Type
Factor
tFTg(Blank)
tFTg
212.4
ng/µl
1.62
DNA
50
tFTg
212.1
ng/µl
1.63
DNA
50
tFTg
206.4
ng/µl
1.58
DNA
50
tFTg
209.1
ng/µl
1.64
DNA
50
tFTg
217.5
ng/µl
1.64
DNA
50
tFTw(Reblank)
tFTw
253.2
ng/µl
1.54
DNA
50
tFTw
249.3
ng/µl
1.54
DNA
50
tFTw
253.2
ng/µl
1.54
DNA
50
tFTw
256.1
ng/µl
1.54
DNA
50
tFTw
254.5
ng/µl
1.54
DNA
50
tFTr(Reblank)
tFTr
170.8
ng/µl
1.53
DNA
50
tFTr
171.8
ng/µl
1.53
DNA
50
tFTr
174.2
ng/µl
1.54
DNA
50
tFTr
171.7
ng/µl
1.53
DNA
50
tFTr
167.6
ng/µl
1.49
DNA
50
tFTb(Reblank)
tFTb
172.6
ng/µl
1.58
DNA
50
tFTb
176.9
ng/µl
1.58
DNA
50
tFTb
175.2
ng/µl
1.57
DNA
50
tFTb
173.8
ng/µl
1.56
DNA
50
tFTb
175.2
ng/µl
1.57
DNA
50
Sample ID
Nucleic Acid
Unit
260/280
Sample Type
Factor
Lg(Blank)
Lg
258.6
ng/µl
1.68
DNA
50
Lg
356.1
ng/µl
1.71
DNA
50
Lg
186.4
ng/µl
1.58
DNA
50
Lg
301.7
ng/µl
1.63
DNA
50
Lg
112.8
ng/µl
1.69
DNA
50
Lw(Reblank)
Lw
261.9
ng/µl
1.57
DNA
50
Lw
263.2
ng/µl
1.57
DNA
50
Lw
317.3
ng/µl
1.57
DNA
50
Lw
302.6
ng/µl
1.52
DNA
50
Lw
263.2
ng/µl
1.58
DNA
50
Lw(Reblank)
Lr
291.3
ng/µl
1.44
DNA
50
Lr
288
ng/µl
1.44
DNA
50
Lr
117.1
ng/µl
1.43
DNA
50
Lr
109.6
ng/µl
1.44
DNA
50
Lr
289.8
ng/µl
1.43
DNA
50
Lb(Reblank)
Lb
324.2
ng/µl
1.55
DNA
50
Lb
239.3
ng/µl
1.55
DNA
50
Lb
317.8
ng/µl
1.53
DNA
50
Lb
339.3
ng/µl
1.54
DNA
50
Lb
354.1
ng/µl
1.55
DNA
50
Sample ID
Nucleic Acid
Unit
260/280
Sample Type
Factor
MTg(Blank)
MTg
200.8
ng/µl
1.68
DNA
50
MTg
209.8
ng/µl
1.68
DNA
50
MTg
203
ng/µl
1.66
DNA
50
MTg
203.4
ng/µl
1.68
DNA
50
MTg
202.5
ng/µl
1.68
DNA
50
MTg(Reblank)
MTw
205.2
ng/µl
1.54
DNA
50
MTw
206.6
ng/µl
1.53
DNA
50
MTw
207.8
ng/µl
1.54
DNA
50
MTw
207.2
ng/µl
1.54
DNA
50
MTw
255.3
ng/µl
1.52
DNA
50
MTr(Reblank)
MTr
107.5
ng/µl
1.51
DNA
50
MTr
117.5
ng/µl
1.41
DNA
50
MTr
116.7
ng/µl
1.53
DNA
50
MTr
106.6
ng/µl
1.59
DNA
50
MTr
113.4
ng/µl
1.53
DNA
50
MTb(Reblank)
MTb
127.6
ng/µl
1.55
DNA
50
MTb
131.4
ng/µl
1.56
DNA
50
MTb
127.6
ng/µl
1.55
DNA
50
MTb
131.1
ng/µl
1.56
DNA
50
MTb
132.4
ng/µl
1.55
DNA
50
MTb
152.1
ng/µl
1.54
DNA
50
Sample ID
Nucleic Acid
Unit
260/280
Sample Type
Factor
Cg(Blank)
Cg
1786.8
ng/µl
1.5
DNA
50
Cg
1810.2
ng/µl
1.45
DNA
50
Cg
1895.7
ng/µl
1.43
DNA
50
Cg
1685
ng/µl
1.44
DNA
50
Cg
1778.2
ng/µl
1.42
DNA
50
Cw(Reblank)
Cw
514
ng/µl
1.46
DNA
50
Cw
516.5
ng/µl
1.46
DNA
50
Cw
519.9
ng/µl
1.46
DNA
50
Cw
515.6
ng/µl
1.45
DNA
50
Cw
521.2
ng/µl
1.44
DNA
50
Cr(Reblank)
Cr
309.9
ng/µl
1.57
DNA
50
Cr
327.8
ng/µl
1.57
DNA
50
Cr
316.4
ng/µl
1.57
DNA
50
Cr
313.2
ng/µl
1.57
DNA
50
Cr
319.6
ng/µl
1.56
DNA
50
Cb(Reblank)
Cb
357.1
ng/µl
1.55
DNA
50
Cb
345
ng/µl
1.56
DNA
50
Cb
345.2
ng/µl
1.56
DNA
50
Cb
344.2
ng/µl
1.56
DNA
50
Cb
348.2
ng/µl
1.56
DNA
50

Next week I’ll work on obtaining averages and plotting the data on graphs which will perhaps make it easier to see what’s happening but from what I can tell the TE Boiling protocols significantly yielded more DNA than any other protocol competing against it. Which is impressive because it’s one of the less elaborate methods to follow.


There are a number of variables that I would like to mention but I’ll do that next week. Until next time, Luis.