Daniel:Notebook/HiResChrPaint/2014-8-20: Difference between revisions
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>Djacobse (Created page with "=Padlock Probes (Started 8/13/2014)= Back to Calendar ==Lambda Exonuclease Digestion== Since ...") |
>Djacobse |
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(5 intermediate revisions by the same user not shown) | |||
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'''Reaction Table''' | '''Reaction Table''' | ||
{| 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:#B8CCE4;font-size:12pt" | |- style="background-color:#B8CCE4;font-size:12pt;font-weight:bold" align="center" | ||
| width=" | | width="93" height="33" | Reagent | ||
| width="65 | | width="65" | PPRL (uL) | ||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
|style="background-color:#FCD5B4" height="15" valign="bottom" | amplicon | |style="background-color:#FCD5B4" height="15" valign="bottom" | amplicon | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 30 | ||
|- style="font-size:12pt" | |||
|style="background-color:#FCD5B4" height="15" valign="bottom" | ug Input | |||
| align="center" align="center" valign="bottom" | 2.0 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
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|- style="font-size:12pt" | |- style="font-size:12pt" | ||
|style="background-color:#FCD5B4" height="15" valign="bottom" | nf H2O | |style="background-color:#FCD5B4" height="15" valign="bottom" | nf H2O | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 45 | ||
|- style="font-size:12pt;font-weight:bold" | |- style="font-size:12pt;font-weight:bold" | ||
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'''DpnII Primer Table''' | '''DpnII Primer Table''' | ||
{| 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:#B8CCE4;font-size:12pt" | |- style="background-color:#B8CCE4;font-size:12pt;font-weight:bold" align="center" | ||
| width=" | | width="93" height="31" | Reagent | ||
| width="65 | | width="65" | PPRL (uL) | ||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
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#Add 5 uL DpnII and incubate at 37C for 2 hours | #Add 5 uL DpnII and incubate at 37C for 2 hours | ||
#Heat inactivate DpnII at 65C for 20 minutes | #Heat inactivate DpnII at 65C for 20 minutes | ||
===Nanodrop Results=== | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#CCC0DA;font-size:12pt" | |||
| width="86" height="28" valign="bottom" | Sample | |||
| width="65" align="center" | ng/uL ssDNA | |||
| width="65" align="center" | ug in 20 uL | |||
| width="65" align="center" | Total | |||
|- style="font-size:12pt" | |||
|style="background-color:#D9D9D9" height="15" valign="bottom" | PPRL-DpnII-A | |||
| align="center" align="center" valign="bottom" | 38.7 | |||
| align="center" align="center" valign="bottom" | 0.8 | |||
| align="center" align="center" valign="bottom" | | |||
|- style="font-size:12pt" | |||
|style="background-color:#D9D9D9" height="15" valign="bottom" | PPRL-DpnII-B | |||
| align="center" align="center" valign="bottom" | 35.3 | |||
| align="center" align="center" valign="bottom" | 0.7 | |||
|style="font-weight:bold" align="center" align="center" valign="bottom" | 1.5 | |||
|} | |||
Should be enough to label with. | |||
[[Category:HRCP]] [[Category:Lambda Exo]] [[Category:DpnII]] [[Category:USER]] [[Category:20140813]] |
Latest revision as of 17:57, 10 September 2014
Padlock Probes (Started 8/13/2014)[edit]
Lambda Exonuclease Digestion[edit]
Since it looks like I might have less DNA than I originally thought (makes sense, several hundred ug is pretty unlikely), I'm going to run the lambda exonuclease digestion on the remaining padlock probes, A and B.
Reaction Table
Reagent | PPRL-A (uL) | PPRL-B (uL) |
Amplicon | 45 | 55 |
ug Input | 20.7 | 25.6 |
Lambda Exo Buffer (10X) | 10 | 10 |
Lambda Exonuclease (5 U/uL) | 5 | 5 |
nf H2O | 40 | 30 |
Total | 100 | 100 |
- Set up reaction according to table
- Incubate at 37C for 2 hours
- Heat inactivate for 10 minutes at 75C
- Purify using ssDNA columns, elute with 20 uL nfH2O
Nanodrop Results[edit]
Sample | ng/uL | ug in 20 uL | Input (ug) | Efficiency (%) | ug Total |
PPRL-A | 132.8 | 2.7 | 20.7 | 12.83 | |
PPRL-B | 214 | 4.3 | 25.6 | 16.72 | 6.9 |
This result is good enough to proceed with.
USER/DpnII Digestion[edit]
Reaction Table
Reagent | PPRL (uL) |
amplicon | 30 |
ug Input | 2.0 |
USER | 5 |
nf H2O | 45 |
Total | 80 |
- Set up reaction according to table in a 0.2 mL PCR tube
- Incubate for 2 hours at 37C
- Add 15 uL according to DpnII Primer table (below)
DpnII Primer Table
Reagent | PPRL (uL) |
10X DpnII Buffer | 10 |
100 uM RE-DpnII-V4 guide oligo | 5 |
Total | 15 |
- Incubate at 94C for 2 minutes
- Cool to 37C and incubate for 3 minutes
- Add 5 uL DpnII and incubate at 37C for 2 hours
- Heat inactivate DpnII at 65C for 20 minutes
Nanodrop Results[edit]
Sample | ng/uL ssDNA | ug in 20 uL | Total |
PPRL-DpnII-A | 38.7 | 0.8 | |
PPRL-DpnII-B | 35.3 | 0.7 | 1.5 |
Should be enough to label with.