Difference between revisions of "Team:Stony Brook/Notebook/Cancer-W7"

Line 1,551: Line 1,551:
 
<h2> 8/13 </h2>
 
<h2> 8/13 </h2>
 
</div>
 
</div>
 +
 +
<h4> Miniprep and gel run of Dean vector </h4>
 +
<ul>
 +
<li> Two preps used Epoch kit </li>
 +
<li> Two preps used Qiagen </li>
 +
</ul>
 
</div>
 
</div>
 +
 +
<div class="column half_size">
 +
<h5> Ran the plasmids on a gel</h5>
 +
<p> Lanes:</p>
 +
<ol>
 +
<li> 1st Epoch </li>
 +
<li> 2nd Epoch </li>
 +
<li> Ladder </li>
 +
<li> 1st Qiagen </li>
 +
<li> 2nd Qiagen </li>
 +
</ol>
 +
<ul>
 +
<li> The gel wells 4 and 5 were contaminated by a little bit of RNA </li>
 +
</ul>
 +
</div>
 +
 +
<div class="column half_size">
 +
<h4> Nanodrop of Miniprepped plasmids </h4>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Concentration (ng/ul) </th>
 +
<th> 260/280 </th>
 +
</tr>
 +
<tr>
 +
<td> 1st Epoch</td>
 +
<td> 133.4 </td>
 +
<td> 1.89 </td>
 +
</tr>
 +
<tr>
 +
<td> 2nd Epoch </td>
 +
<td> 142.6 </td>
 +
<td> 1.92 </td>
 +
</tr>
 +
<tr>
 +
<td> 1st Qiagen </td>
 +
<td> 188.5 </td>
 +
<td> 2.02 </td>
 +
</tr>
 +
<tr>
 +
<td> 2nd Qiagen </td>
 +
<td> 205.6 </td>
 +
<td> 1.97 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
<h4> 50ul Digest of Plasmid and Insert </h4>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h5> Epoch 1 </h5>
 +
</div>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental ul </th>
 +
<th> Control ul </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O </td>
 +
<td> 36.5</td>
 +
<td> 37.5 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 5 </td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> PvuII-HF </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> XhoI </td>
 +
<td> 0.5</td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 7.5 </td>
 +
<td> 7.5 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h5> Epoch 2 </h5>
 +
</div>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental ul </th>
 +
<th> Control ul </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O </td>
 +
<td> 37</td>
 +
<td> 38</td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 5 </td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> PvuII-HF </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> XhoI </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 7.01 </td>
 +
<td> 7.01 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
 +
<div class="column full_size">
 +
<h5> Insert </h5>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental ul </th>
 +
<th> Control ul </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O </td>
 +
<td> 31.5</td>
 +
<td> 32.5</td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 5 </td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> PvuII-HF </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> XhoI </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 12.55 </td>
 +
<td> 12.55 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
  
 
<div class="column full_size">
 
<div class="column full_size">

Revision as of 23:32, 15 August 2016

MENU ▤

Week 7: 8/8 - 8/14

I left you some of the commonly used templates down there under 8/8. Just fill them in as needed. I'll only really have wifi for a few hours on two days between Saturday and Thursday. If you need anything, message me on Facebook and I'll get back to you as soon as I can.

With the warmest love and regards,

~JOSHUA

Week 7: 8/8 - 8/14

PCR Table Template:
    Contents ul
    Phire #
    H2O #
    50 uM F Primer #
    50 uM R Primer #
    #ug/ul Construct #

PCR Settings Template:

    Phase Temperature (°C) Time (sec)
    Initial Denaturation 98 #
    Denaturation 98 #
    Annealing # #
    Extension 72 #
    Final Extension 72 #

Nanodrop Template:

    Content Concentration (ng/ul) 260/280
    Construct # #
    Vector # #

Ligation Template

    Content ul
    10X T4 Buffer #
    Vector # (# ng)
    Construct # (# ng)
    H2O #
    Ligase #

Multiple Digests Template:

This
    Content Experimental ul Control ul
    H2O # #
    Cutsmart # #
    EcoRI-HF # X
    XbaI # X
    DNA # #
Is
    Content Experimental ul Control ul
    H2O # #
    Cutsmart # #
    EcoRI-HF # X
    XbaI # X
    DNA # #

A
    Content Experimental ul Control ul
    H2O # #
    Cutsmart # #
    EcoRI-HF # X
    XbaI # X
    DNA # #
Thing
    Content Experimental ul Control ul
    H2O # #
    Cutsmart # #
    EcoRI-HF # X
    XbaI # X
    DNA # #

8/8

Sequencing

    T1 T2
    5.34 uL H2O 5.34 uL H2O
    1 uL CR-1 Primer 1 1 uL CR-1 Primer 2
    1.66 uL DNA (301.6 ng/uL) 1.66 uL DNA (301.6 ng/uL)

Diluted BioBrick MiniPreps for PCR

    BioBrick Name Concentration (ng/uL) Contents (DNA + water)
    K592009 76.9 1 uL + 6.69 uL water
    B0015 51.7 1 uL + 4.17 uL water
    K1033910 156.5 1 uL + 14.65 uL water
    R0082 49.5 1 uL + 3.95 uL water
    C0012 150.8 1 uL + 14.08 uL water
    J61100 123.0 1 uL + 11.3 uL water
    R0011 56.7 1 uL + 4.67 uL water

PCR of each BioBrick parts (25 uL Q5 MasterMix rxns)

    Contents uL
    10 uM VF2 primer 1.25 uL
    10 uM VR primer 1.25 uL
    DNA 0.5 uL
    Q5 MM 12.5 uL
    Water 19.5 uL

8/9

Gel ran

Lanes:

  1. Ladder
  2. R0011
  3. B001
  4. K1033
  5. R008
  6. J61100
  7. C0012
  8. K592
  • Didn't work

Nanodrop of Miniprepped Plamids:

    Tube # Concentration (ng/ul)
    1 277.3
    2 #
    2 #
    2 #
PCR of Minprepped Plasmids
    Contents ul
    Q5 Buffer 5uL
    H2O 16.25 uL
    10 uM F Primer 1.25 uL
    10 uM R Primer 1.25 uL
    Construct 0.5 uL
    Q5 Polymerase 0.25 uL
    Q5 Polymerase 0.25 uL

PCR Settings:

    Phase Temperature (°C) Time (sec)
    Initial Denaturation 98 30s
    Denaturation 98 20s
    Annealing 56 15s
    Extension 72 30s
    Final Extension 72 60s

8/10

25 ul PCR of Miniprepped Plasmids for Project

    Contents ul
    Q5 Buffer 5
    Q5 Polymerase 5
    H2O 16.25
    10 uM F Primer 1.25
    10 uM R Primer 1.25
    Construct 0.5
    Phase Temperature (°C) Time (sec)
    Initial Denaturation 98 30
    Denaturation 98 20
    Annealing 56 15
    Extension 72 30
    Final Extension 72 60
PCR was run on the following construct concentrations in ng/ul
  • 273
  • 176.5
  • 296.6
  • 311.5
  • 301.6
  • 301.6
  • 259
  • 366.6
  • PCRs did not work → Changed annealing temperature to 66°C
  • Re-ran the first 5 constructs on the above list

25 ul PCR of Miniprepped Plasmid for BioBrick Portion

    Contents ul
    Q5 Master Mix 12.5
    H2O 9.5
    10 uM F Primer 1.25
    10 uM R Primer 1.25
    Template 0.5
  • This setup was used for all BioBrick Parts
  • Ran with the "Sunil" Program with a 66°C annealing temperature

    8/11

    Ran a gel of BioBrick Plasmid PCRs from last night

    Lanes:

    1. BOOi5
    2. ROO82
    3. ROO11
    4. Ja1100
    5. Ladder
    6. K1033910
    7. K592009
    8. COO12
    • Used 8ul of each product was used in each gel

    25ul PCR Run

      Contents ul
      Q5 Buffer 5
      Q5 Polymerase 0.25
      H2O 15.75
      10 uM F Primer 1.25
      10 uM R Primer 1.25
      366.6ug/ul Construct 1ul
    PCR Settings - 35 Cycles
      Phase Temperature (°C) Time (sec)
      Initial Denaturation 98 30
      Denaturation 98 20
      Annealing 65 30
      Extension 72 30
      Final Extension 72 60
    Dilution of 366.6 Plasmid made

    (1ul)(366.6ng/ul) = X(1n/ul)



    Gel of Plasmid PCR

    Lanes:

    1. Ladder
    2. Jonathan Plasmid
    3. Ryan Plasmid - 366.6 dilution
    Ran a PCR purification
    • Used the setup from 8/10
    • Also purified the BioBrick PCRs from 8/10

    Nanodropped the products

      Content Concentration (ng/ul) 260/280
      BOO15 15.1 1.72
      ROO15.1 15.1 1.85
      ROOd1 11.8 1.71
      J61100 11.3 1.61
      K59200 20.3 1.76
      K103340 21.7 1.82
      COO12 23.4 1.9
    Gel of BioBrick PCR

    Lanes:

    1. COO12
    2. ROO11
    3. K1033910
    4. J61100
    5. K592009
    6. ROO82
    7. BOO15

    Digest of Project Plasmids

277.3 ng/ul Template
    Content Experimental ul Control ul
    H2O 40.89 41.39
    3.1 Buffer 5 5
    NotI 0.5 X
    DNA 3.61 3.61
176.5 ng/ul
    Content Experimental ul Control ul
    H2O 38.83 39.33
    3.1 5 5
    NotI 0.5 X
    DNA 5.67 5.67
  • Band expected at 6500bp
296.6 ng/ul
    Content Experimental ul Control ul
    H2O 41.13 41.63
    3.1 5 5
    EcoRI-HF 0.5 X
    DNA 3.37 3.37
311.5 ng/ul
    Content Experimental ul Control ul
    H2O 41.29 41.29
    3.1 5 5
    EcoRI-HF 0.5 X
    DNA 3.21 3.21
  • Band expected at 300bp and 6200
  • Result = 1 band at 5600

8/12

Gels of project plasmid

  • Loaded with 20ul of each product in wells
Gel 1

Lanes:

  1. 277.3 Control
  2. 277.3 Experimental
  3. Ladder
  4. 176.5 Experimental
  5. 176.5 Control
Gel 1

Lanes:

  1. Empty
  2. 296.6 Control
  3. 296.6 Experimental
  4. Ladder
  5. 311.5 Experimental
  6. 311.5 Control


Digested and nanodropped BioBrick parts

Nanodropped the products

    Content Concentration (ng/ul) 260/280
    BOO15 11.9 1.39
    ROO11 10.2 1.38
    ROO82 18.4 1.64
    J61100 14.2 1.35
    K59200 9.5 1.46
    K103340 13.4 1.47
    COO12 13.6 1.47

Gel of PEP352GAP + Jonathan Plasmids

Lanes:

  1. 547
  2. 498.9
  3. Ladder
  4. Balazsi
  5. Transformed Balazsi

Digests of BioBrick Parts - Round 1

ROO11
    Content ul
    Cutsmart 5.5
    SpeI 0.5
    DNA 49
J61100
    Content ul
    Cutsmart 3.98
    XbaI 0.5
    DNA 35.2

K1033910
    Content ul
    Cutsmart 3.98
    SpeI 0.5
    DNA 37.3
BOO15
    Content ul
    Cutsmart 4.75
    XbaI 0.5
    DNA 42.0

ROO82
    Content ul
    Cutsmart 3.1
    SpeI 0.5
    DNA 27.2
561100
    Content ul
    Cutsmart 3.98
    XbaI 0.5
    DNA 35.2

K592009
    Content ul
    Cutsmart 5.9
    SpeI 0.5
    DNA 52.6
561100
    Content ul
    Cutsmart 3.98
    XbaI 0.5
    DNA 35.2

COO12
    Content ul
    Cutsmart 4.3
    SpeI 0.5
    DNA 38.5
BOO15
    Content ul
    Cutsmart 4.75
    XbaI 0.5
    DNA 42.0

PCR of IDT Construct

    Contents ul
    Phire 25
    H2O 22
    50 uM F Primer 1
    50 uM R Primer 1
    DNA Template 1
    Phase Temperature (°C) Time (sec)
    Initial Denaturation 98 30
    Denaturation 98 20
    Annealing 5 30
    Extension 72 30
    Final Extension 72 60

Ran a gel on those products

Lanes:

  1. Ladder
  2. Blank
  3. JK Construct Plasmid
  4. PCR

Nanodropped of PCR

    Content Concentration (ng/ul) 260/280
    Construct 79.7 1.77

8/13

Miniprep and gel run of Dean vector

  • Two preps used Epoch kit
  • Two preps used Qiagen
Ran the plasmids on a gel

Lanes:

  1. 1st Epoch
  2. 2nd Epoch
  3. Ladder
  4. 1st Qiagen
  5. 2nd Qiagen
  • The gel wells 4 and 5 were contaminated by a little bit of RNA

Nanodrop of Miniprepped plasmids

    Content Concentration (ng/ul) 260/280
    1st Epoch 133.4 1.89
    2nd Epoch 142.6 1.92
    1st Qiagen 188.5 2.02
    2nd Qiagen 205.6 1.97

50ul Digest of Plasmid and Insert

Epoch 1
    Content Experimental ul Control ul
    H2O 36.5 37.5
    Cutsmart 5 5
    PvuII-HF 0.5 X
    XhoI 0.5 X
    DNA 7.5 7.5
Epoch 2
    Content Experimental ul Control ul
    H2O 37 38
    Cutsmart 5 5
    PvuII-HF 0.5 X
    XhoI 0.5 X
    DNA 7.01 7.01
Insert
    Content Experimental ul Control ul
    H2O 31.5 32.5
    Cutsmart 5 5
    PvuII-HF 0.5 X
    XhoI 0.5 X
    DNA 12.55 12.55

8/14