Daniel:Notebook/HiResChrPaint/2013-7-18: Difference between revisions
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===Nanodrop Results=== | ===Nanodrop Results=== | ||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="font-size:12pt;font-weight:bold" align="center" | |||
| width="65" height="15" | Sample | |||
| width="65" | V4S4A | |||
| width="65" | V4S4B | |||
| width="65" | V4S4C | |||
| width="65" | V4S4D | |||
| width="65" | V6S4A | |||
| width="65" | V6S4B | |||
| width="65" | V6S4C | |||
| width="65" | V6S4D | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | ng/uL | |||
| align="center" | 87.9 | |||
| align="center" | 89.4 | |||
| align="center" | 83.9 | |||
| align="center" | 86.9 | |||
| align="center" | 101.8 | |||
| align="center" | 102.7 | |||
| align="center" | 89.2 | |||
| align="center" | 89.1 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | ug in 40 uL | |||
| align="center" | 3.5 | |||
| align="center" | 3.6 | |||
| align="center" | 3.4 | |||
| align="center" | 3.5 | |||
| align="center" | 4.1 | |||
| align="center" | 4.1 | |||
| align="center" | 3.6 | |||
| align="center" | 3.6 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | Total ug | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | 13.9 | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | 15.3 | |||
|} | |||
==DpnII Digestion== | ==DpnII Digestion== | ||
1. Prepare Samples | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="font-size:12pt;font-weight:bold" align="center" | |||
| width="65" height="15" | Sample | |||
| width="65" | V4S4A | |||
| width="65" | V4S4B | |||
| width="65" | V4S4C | |||
| width="65" | V4S4D | |||
| width="65" | V6S4A | |||
| width="65" | V6S4B | |||
| width="65" | V6S4C | |||
| width="65" | V6S4D | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | ng/uL | |||
| align="center" | 87.9 | |||
| align="center" | 89.4 | |||
| align="center" | 83.9 | |||
| align="center" | 86.9 | |||
| align="center" | 101.8 | |||
| align="center" | 102.7 | |||
| align="center" | 89.2 | |||
| align="center" | 89.1 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | ug in 35 uL | |||
| align="center" | 3.1 | |||
| align="center" | 3.1 | |||
| align="center" | 2.9 | |||
| align="center" | 3.0 | |||
| align="center" | 3.6 | |||
| align="center" | 3.6 | |||
| align="center" | 3.1 | |||
| align="center" | 3.1 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="30" | uL 10X buffer | |||
| align="center" | 5 | |||
| align="center" | 5 | |||
| align="center" | 5 | |||
| align="center" | 5 | |||
| align="center" | 5 | |||
| align="center" | 5 | |||
| align="center" | 5 | |||
| align="center" | 5 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="30" | uL DpnII (50U/uL) | |||
| align="center" | 2 | |||
| align="center" | 2 | |||
| align="center" | 2 | |||
| align="center" | 2 | |||
| align="center" | 2 | |||
| align="center" | 2 | |||
| align="center" | 2 | |||
| align="center" | 2 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | uL nfH2O | |||
| align="center" | 8 | |||
| align="center" | 8 | |||
| align="center" | 8 | |||
| align="center" | 8 | |||
| align="center" | 8 | |||
| align="center" | 8 | |||
| align="center" | 8 | |||
| align="center" | 8 | |||
|- style="font-size:12pt" align="center" | |||
|style="font-weight:bold" height="15" | Total | |||
| align="center" | 50 | |||
| align="center" | 50 | |||
| align="center" | 50 | |||
| align="center" | 50 | |||
| align="center" | 50 | |||
| align="center" | 50 | |||
| align="center" | 50 | |||
| align="center" | 50 | |||
|} | |||
2. Incubate samples at 37C for 16 hours; 20 minute heat shock at 65C; [[Daniel:Notebook/HiResChrPaint/2013-7-19|Continued]] 7/19/2013]] |
Latest revision as of 00:39, 19 July 2013
S4 Probe Preparation[edit]
Going off the positive results of S3 production, I'm going to expand my pool of dye-labeled probes. Since I haven't done the S4 set in a while, I'll be doing that.
PCR Amplification[edit]
1. Reaction Table
20 nM OligoPool | 2X Kapa SYBR qPCR MM | 100 uM AP1V41U | 100 uM AP2V4 | 100 uM AP1V61U | 100 uM AP2V6 | 2 mM aa-dUTP | H20 | Total Volume | |
per rxn | 0.2 | 50 | 0.4 | 0.4 | 0.4 | 0.4 | 2.5 | 45.7 | 100 |
V4S3 (12.5x) | 2.5 | 625 | 5 | 5 | 0 | 0 | 31 | 581.5 | 1250 |
V6S3 (12.5x) | 2.5 | 625 | 0 | 0 | 5 | 5 | 31 | 581.5 | 1250 |
2. Aliquot 100 uL into each of 12 qPCR tubes 3. PCR protocol: i. PCR 3 min 95C ii. 95C 3 sec iii. 55C 30 sec iv. 72C 20 sec v. plate read vi. goto ii x17 vii. 72C 2 min viii. 16C hold 4. Pooled 3 samples together each (300 uL each, 4 pools per set, 8 total) 5. Ethanol Precipitation, added 900 uL 100% EtOH, 30 uL 3 M NaOAc, 1 uL glycoblue 6. Incubated 4 hours; resuspend in 50 uL nfH20 7. Column Purification, elute with 40 uL EB 8. Measure concentrations in nanodrop
qPCR Results[edit]
Nanodrop Results[edit]
Sample | V4S4A | V4S4B | V4S4C | V4S4D | V6S4A | V6S4B | V6S4C | V6S4D |
ng/uL | 87.9 | 89.4 | 83.9 | 86.9 | 101.8 | 102.7 | 89.2 | 89.1 |
ug in 40 uL | 3.5 | 3.6 | 3.4 | 3.5 | 4.1 | 4.1 | 3.6 | 3.6 |
Total ug | 13.9 | 15.3 |
DpnII Digestion[edit]
1. Prepare Samples
Sample | V4S4A | V4S4B | V4S4C | V4S4D | V6S4A | V6S4B | V6S4C | V6S4D |
ng/uL | 87.9 | 89.4 | 83.9 | 86.9 | 101.8 | 102.7 | 89.2 | 89.1 |
ug in 35 uL | 3.1 | 3.1 | 2.9 | 3.0 | 3.6 | 3.6 | 3.1 | 3.1 |
uL 10X buffer | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 |
uL DpnII (50U/uL) | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
uL nfH2O | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 |
Total | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 |
2. Incubate samples at 37C for 16 hours; 20 minute heat shock at 65C; Continued 7/19/2013]]