Daniel:Notebook/ComboLock/2016-6-30: Difference between revisions
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<li>qPCR</li> | <li>qPCR</li> | ||
<ol type="A"> | <ol type="A"> | ||
< | <li>Set up reaction according to table</li> | ||
</ | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | ||
|- style="background-color:#FCD5B4;font-size:12pt;font-weight:bold" align="center" | |- style="background-color:#FCD5B4;font-size:12pt;font-weight:bold" align="center" | ||
| width=" | | width="85" height="45" | Sample | ||
| width="65" | Lane | | width="65" | Lane | ||
| width="65" | Batch | | width="65" | Batch | ||
Line 39: | Line 38: | ||
| align="center" valign="bottom" | A1 | | align="center" valign="bottom" | A1 | ||
| align="center" valign="bottom" | B1 | | align="center" valign="bottom" | B1 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 10 | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | 25 | | align="center" align="center" valign="bottom" | 25 | ||
Line 51: | Line 50: | ||
| align="center" valign="bottom" | A2 | | align="center" valign="bottom" | A2 | ||
| align="center" valign="bottom" | B2 | | align="center" valign="bottom" | B2 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 11 | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | 25 | | align="center" align="center" valign="bottom" | 25 | ||
Line 63: | Line 62: | ||
| align="center" valign="bottom" | A3 | | align="center" valign="bottom" | A3 | ||
| align="center" valign="bottom" | B3 | | align="center" valign="bottom" | B3 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 12 | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | 25 | | align="center" align="center" valign="bottom" | 25 | ||
Line 75: | Line 74: | ||
| align="center" valign="bottom" | A4 | | align="center" valign="bottom" | A4 | ||
| align="center" valign="bottom" | B4 | | align="center" valign="bottom" | B4 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 13 | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | 25 | | align="center" align="center" valign="bottom" | 25 | ||
Line 87: | Line 86: | ||
| align="center" valign="bottom" | A5 | | align="center" valign="bottom" | A5 | ||
| align="center" valign="bottom" | B5 | | align="center" valign="bottom" | B5 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 14 | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | 25 | | align="center" align="center" valign="bottom" | 25 | ||
Line 99: | Line 98: | ||
| align="center" valign="bottom" | A6 | | align="center" valign="bottom" | A6 | ||
| align="center" valign="bottom" | NTC | | align="center" valign="bottom" | NTC | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 15 | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | 25 | | align="center" align="center" valign="bottom" | 25 | ||
Line 111: | Line 110: | ||
<ol type="a"> | <ol type="a"> | ||
<li>165 uL KAPA SyberFast MM</li> | <li>165 uL KAPA SyberFast MM</li> | ||
<li> | <li>116 uL nfH2O</li> | ||
<li>3.3 uL AmpF 6.4</li></ol> | <li>3.3 uL AmpF 6.4</li></ol> | ||
<li>Add 43 uL Master Mix to each well</li> | <li>Add 43 uL Master Mix to each well</li> | ||
Line 127: | Line 126: | ||
</ol> | </ol> | ||
==Antibody Stage 2 Test 2 (Started [[Daniel:Notebook/ComboLock/2016-6-28#Trial 2|6-28-2016]])= | ===qPCR Results=== | ||
<gallery perrow=2 heights=200px widths=200px> | |||
File:CProbe-VIM-SOD1-20160630.png|qPCR Results | |||
File:2016-06-30-CombolockAb-CProde-VIM-SOD1.jpg|Gel Image | |||
</gallery> | |||
It looks like the right number of samples amplified (One, kinda 2, but it was the wrong lanes. There is a possibility I confused the tubes at some point, so I'll repeat the experiment to see if that is true. | |||
=Antibody Stage 2 Test 2 (Started [[Daniel:Notebook/ComboLock/2016-6-28#Trial 2|6-28-2016]])= | |||
I'm going to get libraries from each of the tests that I have done so far. Since the 6/28 experiment was the most recent antibody test, I'll be using those samples. | |||
<ol start="5"> | <ol start="5"> | ||
<li>Size Selection</li> | <li>Size Selection</li> | ||
<ol type="A"> | <ol type="A"> | ||
<li> | <li>Combine 20 uL sample from each of the seven samples</li> | ||
<li>Add | <li>Add 30 uL 6X loading dye</li> | ||
<li>Aliquot | <li>Aliquot 42 uL each into 4 lanes</li> | ||
<li> | <li>4 uL ladder with 7 uL gel loading dye and 31 uL TBE buffer</li> | ||
<li>Run gel for 25 min at 220V</li> | <li>Run gel for 25 min at 220V</li> | ||
<li>Stain with 3 uL SYBR Gold for 3 min</li> | <li>Stain with 3 uL SYBR Gold for 3 min</li> | ||
<li>Image in gel doc; cut out selected bands and place in 0.5 mL tube with hole in the bottom inside a 1.5 mL tube</li> | <li>Image in gel doc; cut out selected bands and place in 0.5 mL tube with hole in the bottom inside a 1.5 mL tube</li> | ||
<gallery perrow=2 heights=200px widths=200px> | |||
File:2016-06-30-CombolockAb-LP-Test2-SizeSelect.jpg|Before Image | |||
File:2016-06-30-CombolockAb-LP-Test2-SizeSelect-After.jpg|After Image | |||
</gallery> | |||
<li>Centrifuge gel at 14000rpm for 1.5 minutes</li> | <li>Centrifuge gel at 14000rpm for 1.5 minutes</li> | ||
<li>Remove 0.5 mL tube and add 500 uL TE buffer to shredded gel</li> | <li>Remove 0.5 mL tube and add 500 uL TE buffer to shredded gel</li> | ||
Line 150: | Line 164: | ||
<ol type="A"> | <ol type="A"> | ||
<li>Add 1.25 mL 100% EtOH, 50 uL 3M NaOAc, and 2 uL glycoblue to sample</li> | <li>Add 1.25 mL 100% EtOH, 50 uL 3M NaOAc, and 2 uL glycoblue to sample</li> | ||
<li>Incubate overnight at -80C; continued [[Daniel:Notebook/ComboLock/2016- | <li>Incubate overnight at -80C; continued [[Daniel:Notebook/ComboLock/2016-7-1|tomorrow]]</li></ol> | ||
</ol> | </ol> | ||
=C Probe Stage 2 Test Library Prep (From [[Daniel:Notebook/ComboLock/2016-6-25|6-25-2016]])= | |||
Finishing the library prep from the first C probe test. Just combining the samples to be equimolar (since they are the same size I'm assuming equimolar~equimass) | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#DDD9C4;font-size:12pt;font-weight:bold" align="center" | |||
| width="65" height="30" | Batch Source | |||
| width="65" | ng/uL | |||
| width="65" | uL added | |||
| width="65" | final mass (ng) | |||
|- style="font-size:12pt" | |||
| height="15" | Batch2 | |||
| align="center" align="center" | 43.1 | |||
| align="center" align="center" valign="bottom" | 1.3 | |||
| align="center" align="center" valign="bottom" | 55.5 | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
| height="15" | Batch3 | |||
| align="center" align="center" | 11.1 | |||
| align="center" align="center" valign="bottom" | 5 | |||
| align="center" align="center" valign="bottom" | 55.5 | |||
|- style="font-size:12pt" | |||
| height="15" | Batch5 | |||
| align="center" align="center" | 36.1 | |||
| align="center" align="center" valign="bottom" | 1.5 | |||
| align="center" align="center" valign="bottom" | 55.5 | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
| height="15" | Batch6 | |||
| align="center" align="center" | 18.3 | |||
| align="center" align="center" valign="bottom" | 3.0 | |||
| align="center" align="center" valign="bottom" | 55.5 | |||
|} | |||
[[Category:ComboLock]] [[Category:20160628]] [[Category:20160629]] [[Category:20160623]] |
Latest revision as of 22:29, 6 July 2016
C Probe SOD1/VIM Test (Started yesterday)[edit]
Protocol[edit]
- Latch and Padlock Hybridization
- Heat inactivate enzyme by incubating for 2 minutes at 94C
- Exonuclease Digestion
- Prepare exonuclease I/III mix by mixing 15 uL exonuclease I (20 units/μL) and 3 uL exonuclease III (100 units/μL) in 1:1 ratio
- Add 2 μL of exonuclease I/III mix to reaction
- Mix the reaction by swirling pipette around the well 5 times
- Incubate reaction at 37 ºC for 2 hours
- Heat inactivate enzyme by incubating at 94C for 5 minutes
- qPCR
- Set up reaction according to table
- Master Mix
- 165 uL KAPA SyberFast MM
- 116 uL nfH2O
- 3.3 uL AmpF 6.4
- Add 43 uL Master Mix to each well
- qPCR Cycles
- 95C 3 min
- 95C 3 sec
- 55C 30 sec
- 72C 20 sec
- plate read
- goto b x20
- 72C 2 min
- 16C hold
- CProbe-VIM-SOD1-20160630.png
qPCR Results
- 2016-06-30-CombolockAb-CProde-VIM-SOD1.jpg
Gel Image
- Size Selection
- Combine 20 uL sample from each of the seven samples
- Add 30 uL 6X loading dye
- Aliquot 42 uL each into 4 lanes
- 4 uL ladder with 7 uL gel loading dye and 31 uL TBE buffer
- Run gel for 25 min at 220V
- Stain with 3 uL SYBR Gold for 3 min
- Image in gel doc; cut out selected bands and place in 0.5 mL tube with hole in the bottom inside a 1.5 mL tube
- 2016-06-30-CombolockAb-LP-Test2-SizeSelect.jpg
Before Image
- 2016-06-30-CombolockAb-LP-Test2-SizeSelect-After.jpg
After Image
- Centrifuge gel at 14000rpm for 1.5 minutes
- Remove 0.5 mL tube and add 500 uL TE buffer to shredded gel
- Incubate at 37C for at least an hour with vigorous shaking
- Centrifuge at 14000rpm for 1.5 minutes
- Transfer supernatant to a nanosep column
- Centrifuge at 14000rpm for 1.5 minutes
- Transfer flow through to a 2 mL tube
- Ethanol Precipitation
- Add 1.25 mL 100% EtOH, 50 uL 3M NaOAc, and 2 uL glycoblue to sample
- Incubate overnight at -80C; continued tomorrow
Sample | Lane | Batch | AmpR Index | Cells | 2X Kapa SYBR qPCR MM | 100 uM AmpF 6.4 | 10 uM AmpR6.3-IndXX | H2O | Total Volume (uL) |
Sample 1 | A1 | B1 | 10 | 2 | 25 | 0.5 | 5 | 17.5 | 50 |
Sample 2 | A2 | B2 | 11 | 2 | 25 | 0.5 | 5 | 17.5 | 50 |
Sample 3 | A3 | B3 | 12 | 2 | 25 | 0.5 | 5 | 17.5 | 50 |
Sample 4 | A4 | B4 | 13 | 2 | 25 | 0.5 | 5 | 17.5 | 50 |
Sample 5 | A5 | B5 | 14 | 2 | 25 | 0.5 | 5 | 17.5 | 50 |
Sample 6 | A6 | NTC | 15 | 2 | 25 | 0.5 | 5 | 19.5 | 50 |
qPCR Results[edit]
It looks like the right number of samples amplified (One, kinda 2, but it was the wrong lanes. There is a possibility I confused the tubes at some point, so I'll repeat the experiment to see if that is true.
Antibody Stage 2 Test 2 (Started 6-28-2016)[edit]
I'm going to get libraries from each of the tests that I have done so far. Since the 6/28 experiment was the most recent antibody test, I'll be using those samples.
C Probe Stage 2 Test Library Prep (From 6-25-2016)[edit]
Finishing the library prep from the first C probe test. Just combining the samples to be equimolar (since they are the same size I'm assuming equimolar~equimass)
Batch Source | ng/uL | uL added | final mass (ng) |
Batch2 | 43.1 | 1.3 | 55.5 |
Batch3 | 11.1 | 5 | 55.5 |
Batch5 | 36.1 | 1.5 | 55.5 |
Batch6 | 18.3 | 3.0 | 55.5 |