Daniel:Notebook/ComboLock/2016-8-23: Difference between revisions

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<gallery perrow=2 heights=300px widths=300px>
<gallery perrow=2 heights=300px widths=300px>
File:|X2 qPCR Curve
File:20160823-qPCRCurve-X2.png|X2 qPCR Curve
File:2016-08-23-PosConX2.png|X2 Gel Image
File:2016-08-23-PosConX2.png|X2 Gel Image
File:|X3 qPCR Curve
File:20160823-qPCRCurve-X3.png|X3 qPCR Curve
File:2016-08-23-PosConX3.png|X3 Gel Image
File:2016-08-23-PosConX3.png|X3 Gel Image
</gallery>
</gallery>


=Positive Control Amplicon Production=  
=Positive Control Amplicon Production=  
==Protocol==


<ol>
<ol>
Line 350: Line 352:
</ol>
</ol>


===Nanodrop Results===


{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="background-color:#C4BD97;font-size:12pt;font-weight:bold" align="center"
| width="103" height="27" | Sample
| width="77" | ng/uL ssDNA


|- style="font-size:12pt"
| height="15"  valign="bottom" | C1-C2 Amplicon
| align="center" align="center" valign="bottom" | 287.6


|- style="background-color:#D9D9D9;font-size:12pt"
| height="15"  valign="bottom" | C3-C2 Amplicon
| align="center" align="center" valign="bottom" | 331.6


|}
==Protocol (Part 2)==
<ol start="4">
<li>TBE Gel</li>
<ol type="A">
<li>Mix 32 uL TBE and 8 uL 6x Gel Loading dye</li>
<li>Aliquot 10 uL for each sample to parafilm</li>
<li>Add 2 uL of diluted sample/ladder to the drops</li>
<li>Mix with the loading pipette and add 10 uL to each lane</li>
<li>Run for 25 min at 250V</li>
<li>Stain with 3 uL SYBR Gold for 3 min</li>
<li>Rinse and image (see gallery below)</li>
</ol></ol>
[[Image:2016-08-23-PosConAmplicon.png|500px]]
<ol start="5">
<li>Size Select</li>
<ol type="A">
<li>For sample lanes, mix 16 uL sample, 14 uL 6X loading dye and 50 uL TBE (80 uL total)</li>
<li>For ladder lanes, mix 4 uL 25bp ladder, 6 uL 6X loading dye and 30 uL TBE (40 uL total)</li>
<li>Add 20 uL to each lane (2 gels total, 1 per sample)</li>
<li>Run gel for 25 minutes at 250V</li>
<li>While running, prepare tubes by puncturing a 0.5 mL tube with a 0.22 gauge needle and putting inside a 1.5 mL tube</li>
<li>Stain gel for 3 minutes with 3 uL SYBR gold</li>
<li>Image in gel doc</li>
<li>Extract bands at 104 bp and put into tubes; 2 lanes per tube (4 tubes total, 2 per sample)</li>
<li>Image in gel doc post-extraction</li>
<li>Centrifuge tubes at 12000rpm for 1.5 minutes</li>
<li>Discard 0.5 mL tube and resuspend in 500 uL TE buffer</li>
<li>Incubate at 37C for 1 hour with vigorous shaker</li>
<li>Centrifuge at 12000 rpm for 1.5 minutes</li>
<li>Extract the supernatant and place into NanoSep column</li>
<li>Centrifuge at 12000 rpm for 1.5 minutes</li>
</ol>
<li>Ethanol Precipitation</li>
<ol type="A">
<li>Move sample to a fresh 2 mL tube</li>
<li>Add 1250 uL 100% EtOH, 50 uL 3M NaOAc and 2 uL glycoblue</li>
<li>Store at -80C overnight, continued [[Daniel:Notebook/ComboLock/2016-8-24|tomorrow]]</li>
</ol></ol>


[[Category:ComboLock]] [[Category:20160822]]
[[Category:ComboLock]] [[Category:20160822]] [[Category:20160823]]

Latest revision as of 22:42, 26 August 2016

Positive Control Amplicon Test 2 (Started yesterday)[edit]

Back to Calendar

Protocol[edit]

  1. Circularization
    1. Heat inactivate enzyme by incubating for 2 minutes at 94C
  2. Exonuclease Digestion
    1. Prepare exonuclease I/III mix by mixing 20 uL exonuclease I (20 units/μL) and 4 uL exonuclease III (100 units/μL) in 1:1 ratio
    2. Add 2 μL of exonuclease I/III mix to reaction
    3. Mix the reaction by swirling pipette around the well 5 times
    4. Incubate reaction at 37 ºC for 2 hours
    5. Heat inactivate enzyme by incubating at 94C for 5 minutes
  3. qPCR
    1. Set up reaction according to table
    2. Sample Name Lane AmpR Index Sample Vol (uL) 2X Kapa SYBR qPCR MM 100 uM AmpF 6.4 10 uM AmpR6.3-IndXX H2O Total Volume (uL)
      Sample 1 X2-1X A1 33 2 25 0.5 5 17.5 50
      Sample 2 X2-5X B1 34 2 25 0.5 5 17.5 50
      Sample 3 X2-10X C1 35 2 25 0.5 5 17.5 50
      Sample 4 X2-50X D1 36 2 25 0.5 5 17.5 50
      Sample 5 X3-1X E1 37 2 25 0.5 5 17.5 50
      Sample 6 X3-5X F1 38 2 25 0.5 5 17.5 50
      Sample 7 X3-10X G1 39 2 25 0.5 5 17.5 50
      Sample 8 X3-50X H1 40 2 25 0.5 5 17.5 50
      Sample 9 X2Flip A12 41 2 25 0.5 5 17.5 50
      Sample 10 X3Flip B12 42 2 25 0.5 5 17.5 50
      Sample 9 PCR NTC C12 43 2 25 0.5 5 19.5 50
    3. Master Mix
      1. 277.5 uL KAPA SyberFast MM
      2. 194.25 uL nfH2O
      3. 5.55 uL AmpF 6.4
    4. Add 43 uL Master Mix to each well
    5. qPCR Cycles
      1. 95C 3 min
      2. 95C 3 sec
      3. 55C 30 sec
      4. 72C 20 sec
      5. plate read
      6. goto b x20
      7. 72C 2 min
      8. 16C hold

    Results[edit]

    Positive Control Amplicon Production[edit]

    Protocol[edit]

    1. Phosphorylation
      1. In a 0.2 mL tube, add ingredients according to table
      2. Reagent Stock Conc Final Conc./Amount uL added
        AmpLigase Reaction Buffer 10X 1X 2
        ATP 10 mM 1 mM 2
        PCAmp2 100 uM 1 nmol total 10
        T4 DNA Kinase 10 U/uL 10 U 1
        nfH2O NA NA 5
        Total     20
      3. Incubate at 37C for 30 min
    2. Ligation
      1. Set up 2 reactions with the following reagents (DO NOT ADD LIGASE YET)
      2. Reagent Stock Conc Final Conc./Amount uL added
        AmpLigase Reaction Buffer 10X 1X 4
        Latch Oligo 100 uM 500 umol 5
        5' Amplicon Oligo 100 uM 500 umol 5
        Amp Ligase 5 U/uL 5 U 1
        Phosphate Reaction NA NA 10
        nfH2O NA NA 25
        Total     50
      3. Add amplicons according to following table
      4. Sample PCAmp1 PCAmp3 LatchX2 LatchX3
        AmpliconX1 X   X  
        AmpliconX3   X   X
      5. Heat reaction to 95C for 5 min
      6. Lower temp to 55C
      7. Add 1 uL Amp Ligase to each reaction without removing from thermocycler; swirl with pipette tip 5 times to mix
      8. Incubate at 55C for 2 hours
      9. Heat to 95 C to denature dsDNA
      10. Purify with ssDNA column
    3. ssDNA Column
      1. Add 100 uL Binding Buffer to the sample; mix well
      2. Transfer to IIC Column and centrifuge at 14000 rpm for 1 minute; SAVE THE FLOW THROUGH
      3. Add 150 uL 100% EtOH to flow through; mix well
      4. Transfer to IC Column and centrifuge at 14000 rpm for 1 minute; discard flow through
      5. Add 400 uL Prep Buffer and centrifuge at 14000 rpm for 1 minute; discard flow through
      6. Add 700 uL Wash Buffer and centrifuge at 14000 rpm for 1 minute; discard flow through
      7. Add 400 uL Wash Buffer and centrifuge at 14000 rpm for 1 minute; discard flow through
      8. Centrifuge empty column at 14000 rpm for 2 minutes
      9. Transfer to empty 1.5mL centrifuge tube (low bind)
      10. Add 30 uL nfH2O and centrifuge at 14000 rpm for 1 minute

      Nanodrop Results[edit]

      Sample ng/uL ssDNA
      C1-C2 Amplicon 287.6
      C3-C2 Amplicon 331.6

      Protocol (Part 2)[edit]

      1. TBE Gel
        1. Mix 32 uL TBE and 8 uL 6x Gel Loading dye
        2. Aliquot 10 uL for each sample to parafilm
        3. Add 2 uL of diluted sample/ladder to the drops
        4. Mix with the loading pipette and add 10 uL to each lane
        5. Run for 25 min at 250V
        6. Stain with 3 uL SYBR Gold for 3 min
        7. Rinse and image (see gallery below)

      File:2016-08-23-PosConAmplicon.png

      1. Size Select
        1. For sample lanes, mix 16 uL sample, 14 uL 6X loading dye and 50 uL TBE (80 uL total)
        2. For ladder lanes, mix 4 uL 25bp ladder, 6 uL 6X loading dye and 30 uL TBE (40 uL total)
        3. Add 20 uL to each lane (2 gels total, 1 per sample)
        4. Run gel for 25 minutes at 250V
        5. While running, prepare tubes by puncturing a 0.5 mL tube with a 0.22 gauge needle and putting inside a 1.5 mL tube
        6. Stain gel for 3 minutes with 3 uL SYBR gold
        7. Image in gel doc
        8. Extract bands at 104 bp and put into tubes; 2 lanes per tube (4 tubes total, 2 per sample)
        9. Image in gel doc post-extraction
        10. Centrifuge tubes at 12000rpm for 1.5 minutes
        11. Discard 0.5 mL tube and resuspend in 500 uL TE buffer
        12. Incubate at 37C for 1 hour with vigorous shaker
        13. Centrifuge at 12000 rpm for 1.5 minutes
        14. Extract the supernatant and place into NanoSep column
        15. Centrifuge at 12000 rpm for 1.5 minutes
      2. Ethanol Precipitation
        1. Move sample to a fresh 2 mL tube
        2. Add 1250 uL 100% EtOH, 50 uL 3M NaOAc and 2 uL glycoblue
        3. Store at -80C overnight, continued tomorrow