Difference between revisions of "Team:Northwestern/10 03"

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   <article>
 
   <article>
 
     <h1>Monday, October 3<sup>rd</sup></h3>
 
     <h1>Monday, October 3<sup>rd</sup></h3>
−
     <h2>Agenda:</h2>
+
     <h2>Tasks:</h2>
−
 
+
    <div class="row">
 +
      <div class="col-sm-2">
 +
        <p>Jordan</p>
 +
      </div>
 +
      <div class="col-sm-10">
 +
        <ul>
 +
          <li>Ligate YcdO-Cas9 into pSB1C3</li>
 +
          <ul>
 +
            <li>Used a 2:1 molar ratio of insert/backbone</li>
 +
            <ul>
 +
              <li>YcdO-Cas9 with BB ends insert calculated as 3300 bp</li>
 +
              <li>SB1C3 at 2100 bp</li>
 +
            </ul>
 +
            <li>10 uL reaction volume</li>
 +
            <ul>
 +
              <li>Used "YcdO Cas9, EcoRI SpeI PP 10.3" restriction digest from Paul</li>
 +
              <ul>
 +
                <li>2 uL (~80 ng)</li>
 +
              </ul>
 +
              <li>Used pSB1C3 EcoRI/SpeI digest PP</li>
 +
              <ul>
 +
                <li>10.3, 5 uL (25 ng)</li>
 +
              </ul>
 +
              <li>1.5 uL water</li>
 +
              <li>1 uL T4 ligase buffer</li>
 +
              <li>0.5 uL T4 ligase</li>
 +
            </ul>
 +
            <li>Incubating at 25&#176;C for 20 minutes, heat kill at 80&#176;C for 20 minutes</li>
 +
            <li>YcdO concentration in restriction digest was at ~40 ng/ul</li>
 +
          </ul>
 +
          <li>Transform pSB1C3-YcdO-Cas9 into Top10</li>
 +
          <ul>
 +
            <li>Transformed with 3 ul of ligation product</li>
 +
            <li>30 second heat shock</li>
 +
            <li>1 hr 15 recovery</li>
 +
            <li>900uL SOC, plated 450uL</li>
 +
            <li>Plates are titled "YcdO-Cas9 in SB1C3 for sequencing/shipping, TOP10"</li>
 +
          </ul>
 +
          <li>Ligate gRNA template and gRNA guide into pSB1C3</li>
 +
          <ul>
 +
            <li>gRNA guide and gRNA template ratios calculated with 150 bp, SB1C3 calculated with 2100 bp</li>
 +
            <ul>
 +
              <li>Used 2:1 molar ratio of insert:backbone</li>
 +
            </ul>
 +
            <li>10 uL reaction volume</li>
 +
            <ul>
 +
              <li>"gRNA temp EcoRI SpeI PP 10.3," 2 ul (3.6 ng)</li>
 +
              <li>"gRNA EcoRI SpeI PP 10.3," 2 ul (3.6 ng)</li>
 +
              <ul>
 +
                <li>Restriction digest concentrations were diluted:</li>
 +
                <ul>
 +
                  <li>1:5 for gRNA guide</li>
 +
                  <ul>
 +
                    <li>Initial: 230 ng in 25 uL reaction=~9 ng/uL to a concentration of 1.8 ng/ul</li>
 +
                  </ul>
 +
                  <li>1:50 for gRNA temp</li>
 +
                  <ul>
 +
                    <li>Initial conc. 2350ng in 25 uL=~90 ng/uL to a concentration of 1.8 ng/ul</li>
 +
                  </ul>
 +
                </ul>
 +
              </ul>
 +
              <li>Used 5ul of "pSB1C3 EcoRI SpeI PP 10.3" (25 ng)</li>
 +
              <li>1.5 ul water</li>
 +
              <li>1 ul T4 ligase buffer</li>
 +
              <li>0.5 ul T4 ligase</li>
 +
            </ul>
 +
            <li>Incubating 25&#176;C for 20 minutes, heat kill at 80&#176;C for 20 minutes.</li>
 +
          </ul>
 +
          <li>Ligate gRNA template and gRNA guide into pSB1C3 (again)</li>
 +
          <ul>
 +
            <li>Redid above, but calculated both insert ratios with 1100 bp</li>
 +
            <li>Did not dilute RNA guide, used 3 ul for ~27 ng insert</li>
 +
            <li>Did dilute RNA temp 1:10, but then forgot and used undiluted product.</li>
 +
            <li>Increased reaction volume to 20 ul with water, used 2 ul of buffer</li>
 +
            <li>Added 3 ul or 270 ng (ten times as much insert as needed)</li>
 +
          </ul>
 +
          <li>Transform ligated gRNA products into Top10</li>
 +
          <ul>
 +
            <li>Transformed with 3 ul of ligation product</li>
 +
            <li>30 second heat shock</li>
 +
            <li>1 hr 15 recovery</li>
 +
            <li>900 uL SOC, plated 450 uL</li>
 +
            <li>Plates are titled "BBP-mRFP-gRNA-guide/temp-BBs in SB1C3 for seq/shipping, TOP 10"</li>
 +
          </ul>
 +
          <li>Grow up new overnight cultures (2 of each) for pET28a-Cas9 (BL21) and pET28a-DsbA-Cas9 (BL21) and TorA-Cas9 in pSB1C3 (Top10) and DsbA-Cas9 in pSB1C3 (Top10)</li>
 +
          <ul>
 +
            <li>Grew up new cultures in order to re-miniprep for reasonable concentrations</li>
 +
          </ul>
 +
        </ul>
 +
      </div>
 +
    </div>
 +
    <div class="row">
 +
      <div class="col-sm-2">
 +
        <p>Paul</p>
 +
      </div>
 +
      <div class="col-sm-10">
 +
        <ul>
 +
          <li>Transform pSB1C3-Cas9 into JC8031</li>
 +
          <ul>
 +
            <li>Transformed 1 uL of "Cas9 plasmid miniprep MC 9.2.16 358.9 ng/uL" (I forgot to dilute the sample oops) into JC8031, and 50 pg of pUC19 [Amp] control into Top10 as transformation control. Recovered in 900 uL SOC, plated 450 uL.</li>
 +
          </ul>
 +
          <li>Restriction digest for YcdO-Cas9 into pSB1C3</li>
 +
          <ul>
 +
            <li>Used "YcdO SD" from PCR purified box 5 ul=~1 ug DNA, digest with 1 uL EcoRI HF and slightly &lt; 1 uL SpeI HF from Kelly</li>
 +
          </ul>
 +
          <li>Restriction digest for gRNA-template &amp; gRNA-guide into pSB1C3</li>
 +
          <ul>
 +
            <li>10 uL of gRNA 10 JH (23 ng/uL)</li>
 +
            <li>10 uL of "gRNA template MC 9/2 (235 ng/uL)</li>
 +
            <li>5 uL of linearized pSB1C3 from iGEM (25 ng/uL)</li>
 +
            <li>*used 1 uL Spei GQ Promega from box because we ran out of SpeI HF from Kelly* </li>
 +
          </ul>
 +
        </ul>
 +
      </div>
 +
    </div>
 +
    <div class="row">
 +
      <div class="col-sm-2">
 +
        <p>Tasfia</p>
 +
      </div>
 +
      <div class="col-sm-10">
 +
        <ul>
 +
          <li>Miniprep TorA-Cas9 in pSB1C3(Top10) and DsbA-Cas9 in pSB1C3 (Top10)</li>
 +
          <li>Miniprep pET28a-Cas9 (BL21) and pET28a-DsbA-Cas9 (BL21)</li>
 +
          <ul>
 +
            <li>Really low yields</li>
 +
          </ul>
 +
        </ul>
 +
      </div>
 +
    </div>
 +
  </article>
 
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Latest revision as of 15:37, 18 October 2016

Notebook

Monday, October 3rd

Tasks:

Jordan

  • Ligate YcdO-Cas9 into pSB1C3
    • Used a 2:1 molar ratio of insert/backbone
      • YcdO-Cas9 with BB ends insert calculated as 3300 bp
      • SB1C3 at 2100 bp
    • 10 uL reaction volume
      • Used "YcdO Cas9, EcoRI SpeI PP 10.3" restriction digest from Paul
        • 2 uL (~80 ng)
      • Used pSB1C3 EcoRI/SpeI digest PP
        • 10.3, 5 uL (25 ng)
      • 1.5 uL water
      • 1 uL T4 ligase buffer
      • 0.5 uL T4 ligase
    • Incubating at 25°C for 20 minutes, heat kill at 80°C for 20 minutes
    • YcdO concentration in restriction digest was at ~40 ng/ul
  • Transform pSB1C3-YcdO-Cas9 into Top10
    • Transformed with 3 ul of ligation product
    • 30 second heat shock
    • 1 hr 15 recovery
    • 900uL SOC, plated 450uL
    • Plates are titled "YcdO-Cas9 in SB1C3 for sequencing/shipping, TOP10"
  • Ligate gRNA template and gRNA guide into pSB1C3
    • gRNA guide and gRNA template ratios calculated with 150 bp, SB1C3 calculated with 2100 bp
      • Used 2:1 molar ratio of insert:backbone
    • 10 uL reaction volume
      • "gRNA temp EcoRI SpeI PP 10.3," 2 ul (3.6 ng)
      • "gRNA EcoRI SpeI PP 10.3," 2 ul (3.6 ng)
        • Restriction digest concentrations were diluted:
          • 1:5 for gRNA guide
            • Initial: 230 ng in 25 uL reaction=~9 ng/uL to a concentration of 1.8 ng/ul
          • 1:50 for gRNA temp
            • Initial conc. 2350ng in 25 uL=~90 ng/uL to a concentration of 1.8 ng/ul
      • Used 5ul of "pSB1C3 EcoRI SpeI PP 10.3" (25 ng)
      • 1.5 ul water
      • 1 ul T4 ligase buffer
      • 0.5 ul T4 ligase
    • Incubating 25°C for 20 minutes, heat kill at 80°C for 20 minutes.
  • Ligate gRNA template and gRNA guide into pSB1C3 (again)
    • Redid above, but calculated both insert ratios with 1100 bp
    • Did not dilute RNA guide, used 3 ul for ~27 ng insert
    • Did dilute RNA temp 1:10, but then forgot and used undiluted product.
    • Increased reaction volume to 20 ul with water, used 2 ul of buffer
    • Added 3 ul or 270 ng (ten times as much insert as needed)
  • Transform ligated gRNA products into Top10
    • Transformed with 3 ul of ligation product
    • 30 second heat shock
    • 1 hr 15 recovery
    • 900 uL SOC, plated 450 uL
    • Plates are titled "BBP-mRFP-gRNA-guide/temp-BBs in SB1C3 for seq/shipping, TOP 10"
  • Grow up new overnight cultures (2 of each) for pET28a-Cas9 (BL21) and pET28a-DsbA-Cas9 (BL21) and TorA-Cas9 in pSB1C3 (Top10) and DsbA-Cas9 in pSB1C3 (Top10)
    • Grew up new cultures in order to re-miniprep for reasonable concentrations

Paul

  • Transform pSB1C3-Cas9 into JC8031
    • Transformed 1 uL of "Cas9 plasmid miniprep MC 9.2.16 358.9 ng/uL" (I forgot to dilute the sample oops) into JC8031, and 50 pg of pUC19 [Amp] control into Top10 as transformation control. Recovered in 900 uL SOC, plated 450 uL.
  • Restriction digest for YcdO-Cas9 into pSB1C3
    • Used "YcdO SD" from PCR purified box 5 ul=~1 ug DNA, digest with 1 uL EcoRI HF and slightly < 1 uL SpeI HF from Kelly
  • Restriction digest for gRNA-template & gRNA-guide into pSB1C3
    • 10 uL of gRNA 10 JH (23 ng/uL)
    • 10 uL of "gRNA template MC 9/2 (235 ng/uL)
    • 5 uL of linearized pSB1C3 from iGEM (25 ng/uL)
    • *used 1 uL Spei GQ Promega from box because we ran out of SpeI HF from Kelly*

Tasfia

  • Miniprep TorA-Cas9 in pSB1C3(Top10) and DsbA-Cas9 in pSB1C3 (Top10)
  • Miniprep pET28a-Cas9 (BL21) and pET28a-DsbA-Cas9 (BL21)
    • Really low yields