Daniel:Notebook/ComboLock/2017-3-26: Difference between revisions
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=RCA Test= | =RCA Test (Started [[Daniel:Notebook/ComboLock/2017-3-24|March 24]])= | ||
[[Daniel:Notebook/ComboLock|Back to Calendar]] | [[Daniel:Notebook/ComboLock|Back to Calendar]] | ||
==Linear Product Production-Bglii (Started [[Daniel:Notebook/ComboLock/2017-3-25|Yesterday]])== | |||
==Linear Product Production-Bglii== | |||
<ol start="2"> | <ol start="2"> | ||
Line 49: | Line 48: | ||
{| 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:#92CDDC;font-size:12pt;font-weight:bold" align="center" | |- style="background-color:#92CDDC;font-size:12pt;font-weight:bold" align="center" | ||
| width=" | | width="200" height="30" | Reagent | ||
| width="85" | Single Rxn (uL) | | width="85" | Single Rxn (uL) | ||
| width="85" | Master Mix X+ ( | | width="85" | Master Mix X+ (9.2X) | ||
| width="85" | Master Mix X- ( | | width="85" | Master Mix X- (9.2X) | ||
| width="85" | Master Mix Y+ (3.2X) | | width="85" | Master Mix Y+ (3.2X) | ||
| width="85" | Master Mix Y- (3.2X) | | width="85" | Master Mix Y- (3.2X) | ||
| width="85" | Master Mix Z+ (3.2X) | | width="85" | Master Mix Z+ (3.2X) | ||
| width="85" | Master Mix Z- (3.2X) | | width="85" | Master Mix Z- (3.2X) | ||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 71: | Line 66: | ||
| align="center" | Epi (1:10) | | align="center" | Epi (1:10) | ||
| align="center" | Epi (1:10) | | align="center" | Epi (1:10) | ||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
| height="15" valign="bottom" | Circular Product (1X) | | height="15" valign="bottom" | Circular Product (1X) | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 18.4 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
| align="center" align="center" valign="bottom" | 6.4 | | align="center" align="center" valign="bottom" | 6.4 | ||
Line 94: | Line 81: | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 18.4 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
| align="center" align="center" valign="bottom" | 6.4 | | align="center" align="center" valign="bottom" | 6.4 | ||
Line 107: | Line 90: | ||
| height="15" valign="bottom" | RCA Primer (100 uM) | | height="15" valign="bottom" | RCA Primer (100 uM) | ||
| align="center" align="center" valign="bottom" | 2.5 | | align="center" align="center" valign="bottom" | 2.5 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 23 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 23 | ||
| align="center" align="center" valign="bottom" | 8 | | align="center" align="center" valign="bottom" | 8 | ||
| align="center" align="center" valign="bottom" | 8 | | align="center" align="center" valign="bottom" | 8 | ||
Line 121: | Line 100: | ||
| height="15" valign="bottom" | dNTP (1 mM) | | height="15" valign="bottom" | dNTP (1 mM) | ||
| align="center" align="center" valign="bottom" | 5 | | align="center" align="center" valign="bottom" | 5 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 46 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 46 | ||
| align="center" align="center" valign="bottom" | 16 | | align="center" align="center" valign="bottom" | 16 | ||
| align="center" align="center" valign="bottom" | 16 | | align="center" align="center" valign="bottom" | 16 | ||
Line 135: | Line 110: | ||
| height="15" valign="bottom" | 10X Buffer | | height="15" valign="bottom" | 10X Buffer | ||
| align="center" align="center" valign="bottom" | 2 | | align="center" align="center" valign="bottom" | 2 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 18.4 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 18.4 | ||
| align="center" align="center" valign="bottom" | 6.4 | | align="center" align="center" valign="bottom" | 6.4 | ||
| align="center" align="center" valign="bottom" | 6.4 | | align="center" align="center" valign="bottom" | 6.4 | ||
Line 149: | Line 120: | ||
| height="15" valign="bottom" | Phi29 | | height="15" valign="bottom" | Phi29 | ||
| align="center" align="center" valign="bottom" | 1 | | align="center" align="center" valign="bottom" | 1 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
Line 163: | Line 130: | ||
| height="15" valign="bottom" | BSA (10 mg/mL) | | height="15" valign="bottom" | BSA (10 mg/mL) | ||
| align="center" align="center" valign="bottom" | 0.4 | | align="center" align="center" valign="bottom" | 0.4 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 3.68 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 3.68 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
| align="center" align="center" valign="bottom" | 0 | | align="center" align="center" valign="bottom" | 0 | ||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
| height="15" valign="bottom" | nfH2O | | height="15" valign="bottom" | nfH2O | ||
| align="center" align="center" valign="bottom" | 8.1 | | align="center" align="center" valign="bottom" | 8.1 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 65.32 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 65.32 | ||
| align="center" align="center" valign="bottom" | 24 | | align="center" align="center" valign="bottom" | 24 | ||
| align="center" align="center" valign="bottom" | 24 | | align="center" align="center" valign="bottom" | 24 | ||
| align="center" align="center" valign="bottom" | 24 | | align="center" align="center" valign="bottom" | 24 | ||
| align="center" align="center" valign="bottom" | 24 | | align="center" align="center" valign="bottom" | 24 | ||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
Line 197: | Line 156: | ||
|style="font-weight:bold" align="center" align="center" valign="bottom" | 59.52 | |style="font-weight:bold" align="center" align="center" valign="bottom" | 59.52 | ||
|style="font-weight:bold" align="center" align="center" valign="bottom" | 59.52 | |style="font-weight:bold" align="center" align="center" valign="bottom" | 59.52 | ||
|} | |} | ||
<li>Add 16.5 uL master mix to each tube</li> | <li>Add 16.5 uL master mix to each tube</li> | ||
<ol type="a"><li>Samples "A-C" get + master mixes; samples "D-F" get - master mixes</li></ol> | |||
<li>Add 2.5 uL 10 uM RCA primer and to new reaction tubes according to following rules</li> | <li>Add 2.5 uL 10 uM RCA primer and to new reaction tubes according to following rules</li> | ||
<ol type="a"> | <ol type="a"> | ||
<li>"A" samples get LLRC</li> | <li>"A,D" samples get LLRC</li> | ||
<li>"B" samples get LLRC-v03 (Mono-phosphorothiorate)</li> | <li>"B,E" samples get LLRC-v03 (Mono-phosphorothiorate)</li> | ||
<li>" | <li>"C,F" samples get LLRC-v04 (Tri-phosphorothiorate)</li></ol> | ||
<li>Heat reactions up to 95C for 5 min</li> | <li>Heat reactions up to 95C for 5 min</li> | ||
<li>Cool to 55C and incubate for 15 minutes</li> | <li>Cool to 55C and incubate for 15 minutes</li> | ||
Line 217: | Line 173: | ||
{| 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:#CCFF66;font-size:12pt;font-weight:bold" align="center" | |- style="background-color:#CCFF66;font-size:12pt;font-weight:bold" align="center" | ||
| width=" | | width="105" height="30" | Sample | ||
| width="105" | Enzyme | | width="105" | Master Mix | ||
| width=" | | width="100" | Enzyme | ||
| width="100" | Incubation Time (hrs) | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
| height="15" valign="bottom" | X ( | | height="15" valign="bottom" | X (A-F) | ||
| align="center" valign="bottom" | X | |||
| align="center" valign="bottom" | NEB | | align="center" valign="bottom" | NEB | ||
| align="center" align="center" valign="bottom" | 3 | | align="center" align="center" valign="bottom" | 3 | ||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
| height="15" valign="bottom" | Y ( | | height="15" valign="bottom" | Y (A-F) | ||
| align="center" valign="bottom" | Y | |||
| align="center" valign="bottom" | Thermo | | align="center" valign="bottom" | Thermo | ||
| align="center" align="center" valign="bottom" | 3 | | align="center" align="center" valign="bottom" | 3 | ||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
| height="15" valign="bottom" | Z ( | | height="15" valign="bottom" | Z (A-F) | ||
| align="center" valign="bottom" | Z | |||
| align="center" valign="bottom" | Epi (1:10) | | align="center" valign="bottom" | Epi (1:10) | ||
| align="center" align="center" valign="bottom" | 3 | | align="center" align="center" valign="bottom" | 3 | ||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
| height="15" valign="bottom" | P ( | | height="15" valign="bottom" | P (A-F) | ||
| align="center" valign="bottom" | X | |||
| align="center" valign="bottom" | NEB | | align="center" valign="bottom" | NEB | ||
| align="center" align="center" valign="bottom" | 6 | | align="center" align="center" valign="bottom" | 6 | ||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
| height="15" valign="bottom" | Q ( | | height="15" valign="bottom" | Q (A-F) | ||
| align="center" valign="bottom" | X | |||
| align="center" valign="bottom" | NEB | | align="center" valign="bottom" | NEB | ||
| align="center" align="center" valign="bottom" | 12 | | align="center" align="center" valign="bottom" | 12 | ||
Line 250: | Line 212: | ||
<li>Incubate at 65C for 10 minutes;Hold at 10C until next step</li></ol> | <li>Incubate at 65C for 10 minutes;Hold at 10C until next step</li></ol> | ||
[[Category:ComboLock]] [[Category:20170324]] | Continued [[Daniel:Notebook/ComboLock/2017-3-27|tomorrow]] | ||
[[Category:ComboLock]] [[Category:20170322]] [[Category:20170324]] |
Latest revision as of 23:34, 30 March 2017
RCA Test (Started March 24)[edit]
Linear Product Production-Bglii (Started Yesterday)[edit]
- TBE gel
- Mix 64 uL TBE and 16 uL 6X dye
- Aliquot 10 uL on to parafilm per sample/ladder
- Add 2 uL reaction, 1 uL (10 uM) controls, and 1.5 uL ladder to appropriate aliquot File:GelLanes-20170325-LinearProduct.png
- Add 10 uL mix to gel lanes
- Run gel for 24 minutes at 230V
- Stain with 2 uL SYBR gold for 3 minutes
- Rinse and image in gel doc
File:2017-03-26-LinearProductProduction-Bglii.png
That's the right one. However, there is a ton of primer (bottom of the gel), so I'll run a ssDNA column to fix.
- ssDNA column
- Add 50 uL Binding Buffer to the sample; mix well
- Transfer to IIC Column and centrifuge at 14000 rpm for 1 minute; SAVE THE FLOW THROUGH
- Add 70 uL 100% EtOH to flow through; mix well
- Transfer to IC Column and centrifuge at 14000 rpm for 1 minute; discard flow through
- Add 400 uL Prep Buffer and centrifuge at 14000 rpm for 1 minute; discard flow through
- Add 700 uL Wash Buffer and centrifuge at 14000 rpm for 1 minute; discard flow through
- Add 400 uL Wash Buffer and centrifuge at 14000 rpm for 1 minute; discard flow through
- Centrifuge empty column at 14000 rpm for 2 minutes
- Transfer to empty 1.5mL centrifuge tube (low bind)
- Add 20 uL nfH2O and centrifuge at 14000 rpm for 1 minute
- Rolling Circle Amplification
- Prepare master mix according to table below
- Add 16.5 uL master mix to each tube
- Samples "A-C" get + master mixes; samples "D-F" get - master mixes
- Add 2.5 uL 10 uM RCA primer and to new reaction tubes according to following rules
- "A,D" samples get LLRC
- "B,E" samples get LLRC-v03 (Mono-phosphorothiorate)
- "C,F" samples get LLRC-v04 (Tri-phosphorothiorate)
- Heat reactions up to 95C for 5 min
- Cool to 55C and incubate for 15 minutes
- Cool to 30C and add enzyme
- Incubate at 30C for length of time according to table below
- Incubate at 65C for 10 minutes;Hold at 10C until next step
RCA Protocol[edit]
Reagent | Single Rxn (uL) | Master Mix X+ (9.2X) | Master Mix X- (9.2X) | Master Mix Y+ (3.2X) | Master Mix Y- (3.2X) | Master Mix Z+ (3.2X) | Master Mix Z- (3.2X) |
Enzyme | NA | NEB | NEB | Thermo | Thermo | Epi (1:10) | Epi (1:10) |
Circular Product (1X) | 2 | 18.4 | 0 | 6.4 | 0 | 6.4 | 0 |
Linear Product (1X) | 2 | 0 | 18.4 | 0 | 6.4 | 0 | 6.4 |
RCA Primer (100 uM) | 2.5 | 23 | 23 | 8 | 8 | 8 | 8 |
dNTP (1 mM) | 5 | 46 | 46 | 16 | 16 | 16 | 16 |
10X Buffer | 2 | 18.4 | 18.4 | 6.4 | 6.4 | 6.4 | 6.4 |
Phi29 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
BSA (10 mg/mL) | 0.4 | 3.68 | 3.68 | 0 | 0 | 0 | 0 |
nfH2O | 8.1 | 65.32 | 65.32 | 24 | 24 | 24 | 24 |
Total | 20 | 117.8 | 117.8 | 59.52 | 59.52 | 59.52 | 59.52 |
Sample | Master Mix | Enzyme | Incubation Time (hrs) |
X (A-F) | X | NEB | 3 |
Y (A-F) | Y | Thermo | 3 |
Z (A-F) | Z | Epi (1:10) | 3 |
P (A-F) | X | NEB | 6 |
Q (A-F) | X | NEB | 12 |
Continued tomorrow