Daniel:Notebook/PosSequencing/2017-5-8: Difference between revisions
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{| 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:#66FF66;font-size:12pt;font-weight:bold" align="center" | |- style="background-color:#66FF66;font-size:12pt;font-weight:bold" align="center" | ||
| width=" | | width="185" height="30" | Sample | ||
| width=" | | width="95" | Qubit Conc (ug/mL) | ||
| width=" | | width="100" | Amount (nM) | ||
| width=" | | width="100" | Total Amount (fmol) | ||
| width=" | | width="110" | Amplification (Over 5 amol) | ||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
| height="15" valign="bottom" | Barcode Oligo v1 | | height="15" valign="bottom" | Barcode Oligo v1 | ||
| align="center" align="center" valign="bottom" | 9. | | align="center" align="center" valign="bottom" | 9.3 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 300 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 10493 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 2098646 | ||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
| height="15" valign="bottom" | Barcode Oligo v2 | | height="15" valign="bottom" | Barcode Oligo v2 | ||
| align="center" align="center" valign="bottom" | 11.9 | | align="center" align="center" valign="bottom" | 11.9 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 384 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 13427 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 2685364 | ||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
| height="15" valign="bottom" | Barcode Oligo v3 | | height="15" valign="bottom" | Barcode Oligo v3 | ||
| align="center" align="center" valign="bottom" | 8.01 | | align="center" align="center" valign="bottom" | 8.01 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 258 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 9038 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 1807544 | ||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
| height="15" valign="bottom" | NTC | | height="15" valign="bottom" | NTC | ||
| align="center" align="center" valign="bottom" | 0.15 | | align="center" align="center" valign="bottom" | 0.15 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 5 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 169 | ||
| align="center" align="center" valign="bottom" | | | align="center" align="center" valign="bottom" | 33849 | ||
|} | |} | ||
<gallery perrow=2 heights=300px widths=300px</li> | <gallery perrow=2 heights=300px widths=300px</li> | ||
File:|qPCR curves | File:20170508-qPCR-BarcodeOligoProduction-EcoRI.png|qPCR curves | ||
File:2017-05-08-BarcodeOligoProduction-EcoRI.png|Gel image | File:2017-05-08-BarcodeOligoProduction-EcoRI.png|Gel image | ||
</gallery> | </gallery> | ||
==Bead Binding Test== | ==Bead Binding Test== | ||
'''Sample Matrix''' | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#B1A0C7;font-size:12pt;font-weight:bold" align="center" | |||
| width="85" height="30" | Sample # | |||
| width="160" | Condition | |||
| width="85" | Emulsion Y/N | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| align="center" height="15" | 1 | |||
| Barcode Oligo 1 | |||
| N | |||
|- style="background-color:#BFBFBF;font-size:12pt" align="center" valign="bottom" | |||
| align="center" height="15" | 2 | |||
| Barcode Oligo 3 | |||
| N | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| align="center" height="15" | 3 | |||
| Barcode Oligo 1/3 Mix | |||
| N | |||
|} | |||
<ol> | <ol> | ||
Line 117: | Line 142: | ||
<li>Suspend 2 uL (20 ug, ~20M beads) beads in 100 uL Dynabuffer</li> | <li>Suspend 2 uL (20 ug, ~20M beads) beads in 100 uL Dynabuffer</li> | ||
<li>Apply magnet for 30 sec and remove supernatant</li> | <li>Apply magnet for 30 sec and remove supernatant</li> | ||
<li>Suspend in 20 uL Dynabuffer (conc. | <li>Suspend in 20 uL Dynabuffer (conc. 1 ug/uL)</li> | ||
<li>Add | <li>Add 8 uL single barcode oligo or 4 uL each for sample 3 and up to 12 uL nfH<sub>2</sub>O per sample to bead solution; incubate at RT for 15 min</li> | ||
<li>Wash beads with 100 uL wash buffer; vortex to suspend; apply magnet and remove supernatant</li> | <li>Wash beads with 100 uL wash buffer; vortex to suspend; apply magnet and remove supernatant</li> | ||
<li>Repeat wash step</li> | <li>Repeat wash step</li> | ||
</ol> | </ol> | ||
<li>Melting</li> | <li>Melting</li> | ||
<ol type="A"> | <ol type="A"> | ||
<li>Resuspend in 100μL of TE-Triton 0.1% (TE-T)</li> | <li>Resuspend in 100μL of TE-Triton 0.1% (TE-T)</li> | ||
<li>Melt off the complementary DNA strand by incubating the sample at 95°C for 3 minutes</li> | <li>Melt off the complementary DNA strand by incubating the sample at 95°C for 3 minutes</li> | ||
Line 136: | Line 158: | ||
<ol type="A"> | <ol type="A"> | ||
<li>Resuspend beads in 25 uL 4X SSC buffer</li> | <li>Resuspend beads in 25 uL 4X SSC buffer</li> | ||
<li>Make the following dye hybridization buffer</li> | <li>Make the following 3.1X (1X) dye hybridization buffer</li> | ||
<ol type="a"> | <ol type="a"> | ||
<li> | <li>6.2 (2 ea; 6 total) each uL 10 uM dye; dcprobe6-488, dcprobe6-Cy3, dcprobe6-Cy5</li> | ||
<li> | <li>46.5 (15) uL formamide</li> | ||
<li> | <li>12.4 (4) uL nfH<sub>2</sub>O</li></ol> | ||
<li>Incubate probes at 80C for 5 minutes</li> | |||
<li>Add 25 uL fluorescent probe in 60% formamide to each sample</li> | <li>Add 25 uL fluorescent probe in 60% formamide to each sample</li> | ||
<li>Incubate at room temp in the dark for 30 min</li> | <li>Incubate at room temp in the dark for 30 min</li> | ||
<li>Wash twice in 2X SSC</li> | <li>Wash twice in 2X SSC</li> | ||
<li>Resuspend in 40 uL 2XSSC or 20 uL 2X SSC | <li>Resuspend in 40 uL 2XSSC or 20 uL 2X SSC</li> | ||
</ol> | </ol> | ||
</ol> | </ol> | ||
[[Category:PosSeq]] [[Category:20170505]] [[Category:20170508]] [[Category:OligoPrep]] |
Latest revision as of 18:50, 22 May 2017
Probe Production (Started Friday May 5)[edit]
Protocol[edit]
After the success on Friday, I want to redo the production protocol but for the EcoRI primer. This makes it so that I can mix the two in relative quantities and test out the USER cleavage protocol.
- qPCR
- Make 4.2X (1X) master mix with the following reagents
- 4.2 (1) uL 10 uM AP1v4U
- 4.2 (1) uL 10 uM BiotinEcoRI
- 75.6 (18) uL nfH2O
- 105 (25) uL 2X SYBR Fast
- Add 45 uL master mix to each sample
- Add 5 uL barcode oligo according to plate layout File:20170505-PlateLayout-BiotinOligoProduction.png
- qPCR Cycles
- 95C 3 min
- 95C 3 sec
- 55C 30 sec
- 72C 20 sec
- plate read
- goto b x30
- 72C 2 min
- 16C hold
- Qiaquick Column
- Add 250 PB (5X binding buffer) to 50 sample
- Load sample onto column and spin for 1 minute at 14000 rpm; discard flow through
- Add 700 uL PE (wash buffer) to column and spin for 1 minute at 14000 rpm; discard flow through
- Dry spin column for 1 minute at 14000 rpm; discard flow through
- Let stand with cover open in fume hood for ~5 minutes
- Transfer column to a new 1.5 mL eppendorf tube
- Add 35 uL nfH2O to column
- Let stand 1 minute
- Spin for 1 minute at 14000 rpm
- TBE Gel
- Mix 48 uL TBE and 12 uL 6X dye
- Aliquot 10 uL mix to parafilm
- Add 2 uL sample or 1.5 uL ladder to appropriate aliquot
- Add 10 uL mix to appropriate lane
- Run gel at 240V for 24 minutes
- Open gel and stain with 2 uL SYBR gold for 3 minutes
- Rinse and image in gel doc
- Qubit
- Mix 1194 uL dsDNA buffer and 6 uL dye
- Aliquot 190 uL to standard tubes and 199 uL to dye tubes
- Add 10 uL standard or 1 uL dye
- Vortex and spin down
- Let sit 5 minutes in the dark
- Measure in the Qubit
Results[edit]
Sample | Qubit Conc (ug/mL) | Amount (nM) | Total Amount (fmol) | Amplification (Over 5 amol) |
Barcode Oligo v1 | 9.3 | 300 | 10493 | 2098646 |
Barcode Oligo v2 | 11.9 | 384 | 13427 | 2685364 |
Barcode Oligo v3 | 8.01 | 258 | 9038 | 1807544 |
NTC | 0.15 | 5 | 169 | 33849 |
- 20170508-qPCR-BarcodeOligoProduction-EcoRI.png
qPCR curves
- 2017-05-08-BarcodeOligoProduction-EcoRI.png
Gel image
Bead Binding Test[edit]
Sample Matrix
Sample # | Condition | Emulsion Y/N |
1 | Barcode Oligo 1 | N |
2 | Barcode Oligo 3 | N |
3 | Barcode Oligo 1/3 Mix | N |
- Bead Binding
- Suspend 2 uL (20 ug, ~20M beads) beads in 100 uL Dynabuffer
- Apply magnet for 30 sec and remove supernatant
- Suspend in 20 uL Dynabuffer (conc. 1 ug/uL)
- Add 8 uL single barcode oligo or 4 uL each for sample 3 and up to 12 uL nfH2O per sample to bead solution; incubate at RT for 15 min
- Wash beads with 100 uL wash buffer; vortex to suspend; apply magnet and remove supernatant
- Repeat wash step
- Melting
- Resuspend in 100μL of TE-Triton 0.1% (TE-T)
- Melt off the complementary DNA strand by incubating the sample at 95°C for 3 minutes
- Magnet pull-down for 1 minute and remove supernatant
- Add 100 μL of TE-T and mix
- Repeat wash
- Fluorescent Oligo Binding (All samples)
- Resuspend beads in 25 uL 4X SSC buffer
- Make the following 3.1X (1X) dye hybridization buffer
- 6.2 (2 ea; 6 total) each uL 10 uM dye; dcprobe6-488, dcprobe6-Cy3, dcprobe6-Cy5
- 46.5 (15) uL formamide
- 12.4 (4) uL nfH2O
- Incubate probes at 80C for 5 minutes
- Add 25 uL fluorescent probe in 60% formamide to each sample
- Incubate at room temp in the dark for 30 min
- Wash twice in 2X SSC
- Resuspend in 40 uL 2XSSC or 20 uL 2X SSC