Daniel:Notebook/PosSequencing/2017-4-24: Difference between revisions
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<ol> | <ol> | ||
<li>Template DNA Production (Barcode Oligos)</li> | |||
<ol type="A"> | |||
<li>Start with oligo concentrations of 100 uM (100 pmol/uL)</li> | |||
<li>Make dilutions by adding 5 uL into 50 uL (1:10 dilutions)</li> | |||
<li>Dilute 8X times (final concentration 1 pM or 1 amol/uL)</li> | |||
<li>Make oligo solution by adding 5 uL barcode1 (Alexa488) and barcode3(Cy5) since they have low overlap-Final concentration of oligo is 1 pM; adding 10 uL to PCR mix makes it 0.1pM, the suggested concentration from Ion Torrent protocol</li> | |||
<li>Oil Production</li> | <li>Oil Production</li> | ||
<ol type="A"> | <ol type="A"> | ||
Line 31: | Line 37: | ||
</ol> | </ol> | ||
<li>Emulsion PCR</li> | <li>Emulsion PCR</li> | ||
<li>Mix ingredients using the following table (see '''Notes''')</li> | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#CC66FF;font-size:12pt;font-weight:bold" align="center" | |||
| width="250" height="34" | Component | |||
| width="150" | Ion Torrent Concentration | |||
| width="120" | My uL Added | |||
| width="140" | My Final Concentration | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | 5X PCR Buffer (Taq) * | |||
| align="center" valign="bottom" | 1X | |||
| align="center" align="center" valign="bottom" | 20 | |||
| align="center" valign="bottom" | 1X | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |||
| height="15" valign="bottom" | 10 mM dNTPs ** | |||
| align="center" valign="bottom" | 2.5 mM | |||
| align="center" align="center" valign="bottom" | 25 | |||
| align="center" valign="bottom" | 2.5 mM | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | 25 mM MgCl2 | |||
| align="center" valign="bottom" | 3.5 mM | |||
| align="center" align="center" valign="bottom" | 14 | |||
| align="center" valign="bottom" | 3.5 mM | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |||
| height="15" valign="bottom" | 100 uM Primer A (Free primer-Primer 2) | |||
| align="center" valign="bottom" | 9 uM | |||
| align="center" align="center" valign="bottom" | 5 | |||
| align="center" valign="bottom" | 5 uM | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | 10 uM Primer B (Bound primer-Primer 1) | |||
| align="center" valign="bottom" | 0.1 uM | |||
| align="center" align="center" valign="bottom" | 1 | |||
| align="center" valign="bottom" | 0.1 uM | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |||
| height="15" valign="bottom" | Hydrogel beads, 2M/uL | |||
| align="center" valign="bottom" | 50 Million | |||
| align="center" align="center" valign="bottom" | 10 | |||
| align="center" valign="bottom" | 60 M | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Taq? Polymerase (5 U/uL) * | |||
| align="center" valign="bottom" | 90 Units | |||
| align="center" align="center" valign="bottom" | 10 | |||
| align="center" align="center" valign="bottom" | | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |||
| height="30" | DNA template 2nd Dilution (Barcode Oligos) | |||
| align="center" | 0.12 pM | |||
| align="center" align="center" | 10 | |||
| align="center" valign="bottom" | 0.012 fmol total (0.006 fmol each?) | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | 1 M Ammonium Sulfate | |||
| align="center" valign="bottom" | 5 mM | |||
| align="center" align="center" valign="bottom" | 0 | |||
| align="center" align="center" valign="bottom" | 0 | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |||
| height="15" valign="bottom" | 1 mM Spermidine*** | |||
| align="center" valign="bottom" | 100 uM | |||
| align="center" align="center" valign="bottom" | 0 | |||
| align="center" align="center" valign="bottom" | 0 | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | TIPP | |||
| align="center" valign="bottom" | NA | |||
| align="center" align="center" valign="bottom" | 0 | |||
| align="center" align="center" valign="bottom" | 0 | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |||
| height="15" valign="bottom" | Water | |||
| align="center" valign="bottom" | NA | |||
| align="center" align="center" valign="bottom" | 5 | |||
| align="center" valign="bottom" | NA | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Total Volume | |||
| align="center" align="center" valign="bottom" | | |||
|style="font-weight:bold" align="center" valign="bottom" | 100 | |||
| align="center" valign="bottom" | | |||
|} | |||
==Protocol Part 2== | |||
<li>Emulsion Breaking</li> | <li>Emulsion Breaking</li> | ||
<ol type="A"> | |||
<li>With a 200 uL pipette pool the emulsion into a 1.5 mL tube; save the tip and put aside</li> | |||
<li>Add 100 uL isopropyl alcohol (IPA) to tube with 200 uL tip (use new tip)</li> | |||
<li>Draw up IPA with tip from part A, mix to resuspend tip</li> | |||
<li>Vortex the pooled sample in the 1.5 mL tube for 30 seconds</li> | |||
<li>Spin down the sample 13,000 rpm for 5 minutes</li> | |||
<li>Take off oil-IPA mix (top layer) but do not disrupt the oil/aqueous interface</li> | |||
<li>Add 1000 uL IPA and vortex for 30 seconds</li> | |||
<li>Spin down sample at 13,000rpm for 3 minutes</li> | |||
<li>Again remove IPA without disturbing the pellet</li> | |||
<li>Add 500 uL 4X SSC wash buffer to 1.5 mL tube and vortex for 30 seconds</li> | |||
<li>Go back and mix thoroughly by pipetting up and down; the pellet may be hard to resuspend</li> | |||
<li>Leave on 1.5mL mixer at 1300rpm 1 minute</li> | |||
<li>Spin down sample at 13,000rpm for 1 minute</li> | |||
<li>Remove all but 40uL wash buffer</li> | |||
<li>Repeat steps 11 to 15 two times (j to o)</li> | |||
<li>Resuspend in ~100 uL 4X SSC buffer</li></ol> | |||
<li>Fluorescent Bead Binding</li> | <li>Fluorescent Bead Binding</li> | ||
<li>Imaging</li> | <li>Imaging</li> | ||
</ol> | </ol> |
Revision as of 23:54, 24 April 2017
Emulsion PCR
Protocol
This protocol is principally based off the Ion Torrent protocol for emulsion PCR
- Template DNA Production (Barcode Oligos)
- Start with oligo concentrations of 100 uM (100 pmol/uL)
- Make dilutions by adding 5 uL into 50 uL (1:10 dilutions)
- Dilute 8X times (final concentration 1 pM or 1 amol/uL)
- Make oligo solution by adding 5 uL barcode1 (Alexa488) and barcode3(Cy5) since they have low overlap-Final concentration of oligo is 1 pM; adding 10 uL to PCR mix makes it 0.1pM, the suggested concentration from Ion Torrent protocol
- Oil Production
- Start from Monday April 14's oil prep (Span80-4.5%, Tween20-0.1%, TritonX100-0.05% in mineral oil)
- Template-Bead Binding
- Suspend 2.5 uL (25 ug) beads in 100 uL Dynabuffer
- Apply magnet for 30 sec and remove supernatant
- Suspend 2.5 uL (25 ug) beads in 20 uL Dynabuffer (conc. 1 ug/uL)
- Add 10 uL 1 uM (10 pmol total, 10X excess) template oligo and 10 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
- Resuspend beads in 30 uL TE buffer
- Mix together the three suspensions of beads with different oligos
- Oil-Aqueous Mixing
- Mix 20 uL aqueous into 200 uL oil mixture
- Vortex for 30 seconds
- Repeat mixing to 100 uL (5 times)
- Mix with vortexer for 3 minutes
- Dilute with pure mineral oil for imaging (1:100)
- Emulsion PCR
- Mix ingredients using the following table (see Notes)
- Emulsion Breaking
- With a 200 uL pipette pool the emulsion into a 1.5 mL tube; save the tip and put aside
- Add 100 uL isopropyl alcohol (IPA) to tube with 200 uL tip (use new tip)
- Draw up IPA with tip from part A, mix to resuspend tip
- Vortex the pooled sample in the 1.5 mL tube for 30 seconds
- Spin down the sample 13,000 rpm for 5 minutes
- Take off oil-IPA mix (top layer) but do not disrupt the oil/aqueous interface
- Add 1000 uL IPA and vortex for 30 seconds
- Spin down sample at 13,000rpm for 3 minutes
- Again remove IPA without disturbing the pellet
- Add 500 uL 4X SSC wash buffer to 1.5 mL tube and vortex for 30 seconds
- Go back and mix thoroughly by pipetting up and down; the pellet may be hard to resuspend
- Leave on 1.5mL mixer at 1300rpm 1 minute
- Spin down sample at 13,000rpm for 1 minute
- Remove all but 40uL wash buffer
- Repeat steps 11 to 15 two times (j to o)
- Resuspend in ~100 uL 4X SSC buffer
- Fluorescent Bead Binding
- Imaging
Component | Ion Torrent Concentration | My uL Added | My Final Concentration |
5X PCR Buffer (Taq) * | 1X | 20 | 1X |
10 mM dNTPs ** | 2.5 mM | 25 | 2.5 mM |
25 mM MgCl2 | 3.5 mM | 14 | 3.5 mM |
100 uM Primer A (Free primer-Primer 2) | 9 uM | 5 | 5 uM |
10 uM Primer B (Bound primer-Primer 1) | 0.1 uM | 1 | 0.1 uM |
Hydrogel beads, 2M/uL | 50 Million | 10 | 60 M |
Taq? Polymerase (5 U/uL) * | 90 Units | 10 | |
DNA template 2nd Dilution (Barcode Oligos) | 0.12 pM | 10 | 0.012 fmol total (0.006 fmol each?) |
1 M Ammonium Sulfate | 5 mM | 0 | 0 |
1 mM Spermidine*** | 100 uM | 0 | 0 |
TIPP | NA | 0 | 0 |
Water | NA | 5 | NA |
Total Volume | 100 |