Daniel:Notebook/ComboLock/2016-7-7: Difference between revisions
Jump to navigation
Jump to search
>Djacobse |
>Djacobse |
||
(6 intermediate revisions by the same user not shown) | |||
Line 49: | Line 49: | ||
| align="center" align="center" | 243.1 | | align="center" align="center" | 243.1 | ||
| align="center" align="center" | 15 | | align="center" align="center" | 15 | ||
| align="center" align="center" | 3. | | align="center" align="center" | 3.6 | ||
|- style="background-color:#D9D9D9;font-size:12pt" | |- style="background-color:#D9D9D9;font-size:12pt" | ||
Line 55: | Line 55: | ||
| align="center" align="center" | 287.9 | | align="center" align="center" | 287.9 | ||
| align="center" align="center" | 15 | | align="center" align="center" | 15 | ||
| align="center" align="center" | 4. | | align="center" align="center" | 4.3 | ||
|} | |} | ||
Sample Name: '''DEJ-CL-C03''' | Sample Name: '''DEJ-CL-C03''' | ||
[[Category:ComboLock]] [[Category:20160705]] | |||
=C Probe/Antibody Mix= | |||
I think it is time to try an experiment with the C-Probes and antibodies. Just to get sequence information, if we can. I think I will stick to the sequential hybridization method for now. | |||
==Buffer Prep== | |||
Prepare 1 mL of hybridization buffer and aliquot in 100 uL fractions. Freeze unused. | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#C4D79B;font-size:12pt;font-weight:bold" align="center" | |||
| width="114" height="30" | Reagent | |||
| width="106" | Stock | |||
| width="65" | Final | |||
| width="65" | Dilution | |||
| width="65" | Amt in 100 uL (uL) | |||
| width="65" | Amt in 1 mL (uL) | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Oligos | |||
| align="center" valign="bottom" | 100 uM | |||
| align="center" valign="bottom" | 100 nM | |||
| align="center" align="center" valign="bottom" | 1000 | |||
| align="center" valign="bottom" | 1 uL | |||
| align="center" align="center" valign="bottom" | 0 | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Antibodies | |||
| align="center" valign="bottom" | 1500 nM | |||
| align="center" valign="bottom" | 0.5 nM | |||
| align="center" align="center" valign="bottom" | 3000 | |||
| align="center" valign="bottom" | 1 uL | |||
| align="center" align="center" valign="bottom" | 0 | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | BSA | |||
| align="center" valign="bottom" | 50 mg/mL (5%) | |||
| align="center" align="center" valign="bottom" | 0.10% | |||
| align="center" align="center" valign="bottom" | 500 | |||
| align="center" align="center" valign="bottom" | 0.5 | |||
| align="center" align="center" valign="bottom" | 2 | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | RNAsin | |||
| align="center" valign="bottom" | 40000 U/mL | |||
| align="center" valign="bottom" | 40 U/mL | |||
| align="center" align="center" valign="bottom" | 1000 | |||
| align="center" align="center" valign="bottom" | 0.1 | |||
| align="center" align="center" valign="bottom" | 1 | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | EDTA | |||
| align="center" valign="bottom" | 500 mM | |||
| align="center" valign="bottom" | 5 mM | |||
| align="center" align="center" valign="bottom" | 100 | |||
| align="center" align="center" valign="bottom" | 1 | |||
| align="center" align="center" valign="bottom" | 10 | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Salmon Sperm DNA | |||
| align="center" valign="bottom" | 10 mg/mL | |||
| align="center" valign="bottom" | 0.1 mg/mL | |||
| align="center" align="center" valign="bottom" | 100 | |||
| align="center" valign="bottom" | 1 uL | |||
| align="center" align="center" valign="bottom" | 10 | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | PBS | |||
| align="center" valign="bottom" | 10X | |||
| align="center" valign="bottom" | 1X | |||
| align="center" align="center" valign="bottom" | 10 | |||
| align="center" valign="bottom" | 10 uL | |||
| align="center" align="center" valign="bottom" | 100 | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | nf H2O | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | 85 uL | |||
| align="center" align="center" valign="bottom" | 877 | |||
|} | |||
'''Stringent Wash Buffer''' | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#C4D79B;font-size:12pt;font-weight:bold" align="center" | |||
| width="110" height="42" | Reagent | |||
| width="65" | Stock | |||
| width="65" | Final | |||
| width="65" | Dilution | |||
| width="74" | Amt in 1 mL (uL) | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | PBS | |||
| align="center" valign="bottom" | 10X | |||
| align="center" valign="bottom" | 1X | |||
| align="center" align="center" valign="bottom" | 10 | |||
| align="center" valign="bottom" | 100 uL | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | SSC | |||
| align="center" valign="bottom" | 20X | |||
| align="center" valign="bottom" | 4X | |||
| align="center" align="center" valign="bottom" | 5 | |||
| align="center" valign="bottom" | 200 uL | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Rnasin | |||
| align="center" valign="bottom" | 40000 U/mL | |||
| align="center" valign="bottom" | 40 U/mL | |||
| align="center" align="center" valign="bottom" | 1000 | |||
| align="center" valign="bottom" | 1 uL | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | nf H2O | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | 700 uL | |||
|} | |||
'''LPH Buffer''' | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#C4D79B;font-size:12pt;font-weight:bold" align="center" | |||
| width="110" height="42" | Reagent | |||
| width="65" | Stock | |||
| width="65" | Final | |||
| width="65" | Dilution | |||
| width="90" | Amt in 1 mL (uL) | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Oligos | |||
| align="center" valign="bottom" | 100 uM | |||
| align="center" valign="bottom" | 100 nM | |||
| align="center" align="center" valign="bottom" | 1000 | |||
| align="center" valign="bottom" | 1 uL | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | SSC | |||
| align="center" valign="bottom" | 20X | |||
| align="center" valign="bottom" | 1X | |||
| align="center" align="center" valign="bottom" | 20 | |||
| align="center" valign="bottom" | 50 uL | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | Rnasin | |||
| align="center" valign="bottom" | 40000 U/mL | |||
| align="center" valign="bottom" | 40 U/mL | |||
| align="center" align="center" valign="bottom" | 1000 | |||
| align="center" valign="bottom" | 1 uL | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | PBS | |||
| align="center" valign="bottom" | 10X | |||
| align="center" valign="bottom" | 1X | |||
| align="center" align="center" valign="bottom" | 10 | |||
| align="center" valign="bottom" | 100 uL | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" valign="bottom" | nf H2O | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | NA | |||
| align="center" valign="bottom" | 850 uL | |||
|} | |||
==Protocol== | |||
<ol> | |||
<li>Hybridization</li> | |||
<ol type="A"> | |||
<li>Measure cell concentration using 10 uL cell sample in 90 uL nfH2O</li> | |||
<ol type="a"><li>Human- cells/mL</li></ol> | |||
<li>Extract cells to a new tube such that there are 100000 cells present</li> | |||
<ol type="a"><li>Human- uL; Mouse-85 uL</li></ol> | |||
<li>Pellet cells via centrifugation at 600g for 3 min</li> | |||
<li>Add 200 uL Wash Buffer (0.05% Tween 20 in 1X PBS)</li> | |||
<li>Pellet cells via centrifugation at 600g for 3 min</li> | |||
<li>Resuspend cells in 100 uL hybridization buffer</li> | |||
<li>C Probe preparation</li> | |||
<ol type="a"> | |||
<li>Mix all probes, 1 uL of each 100 uM probe (4 uL total VIM+SOD1 C1 and C2)</li> | |||
<li>Add 6 uL nfH2O to bring concentration to 10 uM for each probe</li> | |||
<li>Incubate at 90C for 5 min; chill on ice to quench</li></ol> | |||
<li>Antibody Prep</li> | |||
<ol type="a"> | |||
<li>Add 1 uL of VIM-PA and VIM-PB each to 0.2 mL tube</li> | |||
<li>Add 28 uL nfH2O (reduces concentration to ~50 nM for each)</li></ol> | |||
<li>Add 1 uL each probe mix according to sample matrix</li> | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="font-size:12pt" align="center" | |||
| align="center" width="85" height="30" | | |||
|style="background-color:#CCC0DA;font-weight:bold" width="65" | C Probes (1 uL each) | |||
|style="background-color:#CCC0DA;font-weight:bold" width="65" | Antibodies (1 uL each) | |||
|style="background-color:#CCC0DA;font-weight:bold" width="65" | U87MG | |||
|style="background-color:#CCC0DA;font-weight:bold" width="65" | 3T3 Cells | |||
|- style="font-size:12pt" | |||
| height="15" | Sample 1 | |||
| align="center" | X | |||
| align="center" | X | |||
| align="center" | X | |||
| align="center" align="center" | | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
| height="15" | Sample 2 | |||
| align="center" align="center" | | |||
| align="center" align="center" | | |||
| align="center" | X | |||
| align="center" align="center" | | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Sample 3 | |||
| align="center" | X | |||
| align="center" | X | |||
| align="center" align="center" | | |||
| align="center" | X | |||
|- style="background-color:#D9D9D9;font-size:12pt" | |||
| height="15" valign="bottom" | Sample 4 | |||
| align="center" align="center" | | |||
| align="center" align="center" | | |||
| align="center" align="center" | | |||
| align="center" | X | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Sample 5 | |||
| align="center" valign="bottom" | X | |||
| align="center" valign="bottom" | X | |||
| align="center" align="center" valign="bottom" | | |||
| align="center" align="center" valign="bottom" | | |||
|} | |||
<li>Incubate probes at 40C for 1 hour with vigorous agitation</li> | |||
<li>Wash three times with 200 uL wash buffer and pelleting at 600xg for 3 min</li> | |||
<li>Incubate cells for 20 min at 40C in 200 uL stringent wash buffer</li> | |||
</ol> | |||
<li>Latch and Padlock Hybridization</li> | |||
<ol type="A"> | |||
<li>Pellet at 600xg for 3 min and remove supernatant</li> | |||
<li>Resuspend pellet in 100 uL LPH buffer with 100 nM Latch0001</li> | |||
<li>Incubate for 30 min at 37C</li> | |||
<li>Wash twice with 200 uL wash buffer</li> | |||
<ol type="a"><li>Wash by pelleting cells at 600xg for 3 min</li></ol> | |||
<li>Resuspend pellet in 100 uL LPH buffer with 100 nM Padlock0001-68</li> | |||
<li>Incubate for 30 min at 37C</li> | |||
<li>Wash twice with 200 uL wash buffer</li> | |||
<ol type="a"><li>Wash by pelleting cells at 600xg for 3 min</li></ol> | |||
<li>Resuspend with 20 uL 1x Amp Ligase buffer</li></ol> | |||
<li>Circularization</li> | |||
<ol type="A"> | |||
<li>Prepare 20 uL KLN mix</li> | |||
<li>Add 2 uL KLN mix to 20 uL of reaction</li> | |||
<li>Incubate at 55C overnight (XX hours) </li> | |||
<li>Continued [[Daniel:Notebook/ComboLock/2016-7-8|tomorrow]]</li> | |||
</ol> | |||
[[Category:ComboLock]] [[Category:20160705]] [[Category:20160707]] |
Latest revision as of 16:39, 8 July 2016
Sequential Hybridization Test (Started 7-5-2016)[edit]
Protocol[edit]
- Ethanol precipitation (from yesterday)
- Centrifuge at 4 C for 25 minutes at 14000 rpm
- Remove supernatant and add 750 uL chilled 75% EtOH
- Centrifuge for 15 minutes at minutes at 4 C at 14000 rpm
- Remove supernatant and dry the pellet in the hood
- Resuspend pellet in 20 uL volume nfH20
- Measure in Nanodrop
- Store DNA at 4C
Nanodrop Results[edit]
Source | ng/uL |
C Probe-Seq Tube 1 | 243.1 |
C Probe-Seq Tube 2 | 287.9 |
Library Prep[edit]
Mixed samples according to table.
Sample | ng/uL | uL added | final mass (ug) |
C Probe-Seq Tube 1 | 243.1 | 15 | 3.6 |
C Probe-Seq Tube 2 | 287.9 | 15 | 4.3 |
Sample Name: DEJ-CL-C03
C Probe/Antibody Mix[edit]
I think it is time to try an experiment with the C-Probes and antibodies. Just to get sequence information, if we can. I think I will stick to the sequential hybridization method for now.
Buffer Prep[edit]
Prepare 1 mL of hybridization buffer and aliquot in 100 uL fractions. Freeze unused.
Reagent | Stock | Final | Dilution | Amt in 100 uL (uL) | Amt in 1 mL (uL) |
Oligos | 100 uM | 100 nM | 1000 | 1 uL | 0 |
Antibodies | 1500 nM | 0.5 nM | 3000 | 1 uL | 0 |
BSA | 50 mg/mL (5%) | 0.10% | 500 | 0.5 | 2 |
RNAsin | 40000 U/mL | 40 U/mL | 1000 | 0.1 | 1 |
EDTA | 500 mM | 5 mM | 100 | 1 | 10 |
Salmon Sperm DNA | 10 mg/mL | 0.1 mg/mL | 100 | 1 uL | 10 |
PBS | 10X | 1X | 10 | 10 uL | 100 |
nf H2O | NA | NA | NA | 85 uL | 877 |
Stringent Wash Buffer
Reagent | Stock | Final | Dilution | Amt in 1 mL (uL) |
PBS | 10X | 1X | 10 | 100 uL |
SSC | 20X | 4X | 5 | 200 uL |
Rnasin | 40000 U/mL | 40 U/mL | 1000 | 1 uL |
nf H2O | NA | NA | NA | 700 uL |
LPH Buffer
Reagent | Stock | Final | Dilution | Amt in 1 mL (uL) |
Oligos | 100 uM | 100 nM | 1000 | 1 uL |
SSC | 20X | 1X | 20 | 50 uL |
Rnasin | 40000 U/mL | 40 U/mL | 1000 | 1 uL |
PBS | 10X | 1X | 10 | 100 uL |
nf H2O | NA | NA | NA | 850 uL |
Protocol[edit]
- Hybridization
- Measure cell concentration using 10 uL cell sample in 90 uL nfH2O
- Human- cells/mL
- Extract cells to a new tube such that there are 100000 cells present
- Human- uL; Mouse-85 uL
- Pellet cells via centrifugation at 600g for 3 min
- Add 200 uL Wash Buffer (0.05% Tween 20 in 1X PBS)
- Pellet cells via centrifugation at 600g for 3 min
- Resuspend cells in 100 uL hybridization buffer
- C Probe preparation
- Mix all probes, 1 uL of each 100 uM probe (4 uL total VIM+SOD1 C1 and C2)
- Add 6 uL nfH2O to bring concentration to 10 uM for each probe
- Incubate at 90C for 5 min; chill on ice to quench
- Antibody Prep
- Add 1 uL of VIM-PA and VIM-PB each to 0.2 mL tube
- Add 28 uL nfH2O (reduces concentration to ~50 nM for each)
- Add 1 uL each probe mix according to sample matrix
- Incubate probes at 40C for 1 hour with vigorous agitation
- Wash three times with 200 uL wash buffer and pelleting at 600xg for 3 min
- Incubate cells for 20 min at 40C in 200 uL stringent wash buffer
- Latch and Padlock Hybridization
- Pellet at 600xg for 3 min and remove supernatant
- Resuspend pellet in 100 uL LPH buffer with 100 nM Latch0001
- Incubate for 30 min at 37C
- Wash twice with 200 uL wash buffer
- Wash by pelleting cells at 600xg for 3 min
- Resuspend pellet in 100 uL LPH buffer with 100 nM Padlock0001-68
- Incubate for 30 min at 37C
- Wash twice with 200 uL wash buffer
- Wash by pelleting cells at 600xg for 3 min
- Resuspend with 20 uL 1x Amp Ligase buffer
- Circularization
- Prepare 20 uL KLN mix
- Add 2 uL KLN mix to 20 uL of reaction
- Incubate at 55C overnight (XX hours)
- Continued tomorrow
C Probes (1 uL each) | Antibodies (1 uL each) | U87MG | 3T3 Cells | |
Sample 1 | X | X | X | |
Sample 2 | X | |||
Sample 3 | X | X | X | |
Sample 4 | X | |||
Sample 5 | X | X |