Daniel:Notebook/PosSequencing/2017-5-19: Difference between revisions
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>Djacobse (Created page with "=Double Stranded Probe Production= Back to Calendar I need to make more of these. ==Protocol== <ol> <li>qPCR</li> <ol type="A"> <li>Make ...") |
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| height="15" valign="bottom" | Barcode Oligo v2 | | height="15" valign="bottom" | Barcode Oligo v2 | ||
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| height="15" valign="bottom" | Barcode Oligo v3 | | height="15" valign="bottom" | Barcode Oligo v3 | ||
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| height="15" valign="bottom" | NTC | | height="15" valign="bottom" | NTC | ||
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<gallery perrow=2 heights=300px widths=300px</li> | <gallery perrow=2 heights=300px widths=300px</li> | ||
File: | File:|qPCR curves</li> | ||
File: | File:|Gel image | ||
</gallery> | </gallery> |
Revision as of 15:48, 19 May 2017
Double Stranded Probe Production
I need to make more of these.
Protocol
- qPCR
- Make three 8.2X (1X) master mix with the following reagents
- 8.2 (1) uL 10 uM AP1v4U
- 8.2 (1) uL 10 uM BiotinU
- 172.2 (21) uL nfH2O
- 205 (25) uL 2X SYBR Fast
- 16.4 (2) appropriate barcode oligo (100 pM)
- Add 50 uL master mix to 8 lanes per sample [[Image:|600px]]
- 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 Note: I will be pooling samples and double loading columns, yielding 4 samples per column (2 columns per barcode oligo, 6 columns total)
- Pool 2 samples and 500 uL PB (5X binding buffer)
- Load sample onto column and spin for 1 minute at 14000 rpm; discard flow through
- Add another 600 uL pooled sample to columnand 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
- Pool samples when finished; concentrate if desired
- 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
Sample | Qubit Conc (ug/mL) | Amount (nM) | Total Amount (fmol) | Amplification (Over 5 amol) |
Barcode Oligo v1 | ||||
Barcode Oligo v2 | ||||
Barcode Oligo v3 | ||||
NTC |