Team:HokkaidoU Japan/Notebook/Protocols

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<ul>
<ul>
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<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey">High-School</a></li>
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<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey">High School</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Education">Education</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Education">Education</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Survey">Survey</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Survey">Survey</a></li>
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<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion">Discussion</a></li>
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion">Discussion</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Background">Background</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Background">Background</a></li>
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<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Estimation">Evaluation</a></li>
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<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Evaluation">Evaluation</a></li>
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   <li>Incubate on ice for 30 min.</li>
   <li>Incubate on ice for 30 min.</li>
   <li>Add (600)  &micro;L  of LB.</li>
   <li>Add (600)  &micro;L  of LB.</li>
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   <li>(Incubate the cells for 2 hrs at 37C.)</li>
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   <li>(Incubate the cells for 2 hrs at 37&#8451;.)</li>
   <li>Spread 300  &micro;L  of the culture onto plate with LB and appropriate antibiotics.</li>
   <li>Spread 300  &micro;L  of the culture onto plate with LB and appropriate antibiotics.</li>
   <li>(Add 900  &micro;L  of LB to 100  &micro;L  of the culture and spread 300  &micro;L  of it onto second plate.)</li>
   <li>(Add 900  &micro;L  of LB to 100  &micro;L  of the culture and spread 300  &micro;L  of it onto second plate.)</li>
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   <li>Incubate the plate(s) at 37C for 16~20 hours.</li>
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   <li>Incubate the plate(s) at 37&#8451; for 16~20 hours.</li>
</ol>
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<ol>
<ol>
   <li>Add (5)  &micro;L  of NaOAc, 1.5  &micro;L  of glycogen and (125)  &micro;L  of 100% ethanol.</li>
   <li>Add (5)  &micro;L  of NaOAc, 1.5  &micro;L  of glycogen and (125)  &micro;L  of 100% ethanol.</li>
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   <li>(Leave it at -80C for 1 hr. / Soak liquid nitrogen in an instant.)</li>
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   <li>(Leave it at -80&#8451; for 1 hr. / Soak liquid nitrogen in an instant.)</li>
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   <li>Centrifuge at 15,000 rpm for (10~15) min at 4C.</li>
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   <li>Centrifuge at 15,000 rpm for (10~15) min at 4&#8451;.</li>
   <li>Remove supernatant and add (220)  &micro;L  of 70% ethanol.</li>
   <li>Remove supernatant and add (220)  &micro;L  of 70% ethanol.</li>
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   <li>Centrifuge at 15,000 rpm for (5~15) min at 4C.</li>
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   <li>Centrifuge at 15,000 rpm for (5~15) min at 4&#8451;.</li>
   <li>Remove supernatant and air-dry at room temperature with light sheilding.</li>
   <li>Remove supernatant and air-dry at room temperature with light sheilding.</li>
   <li>Suspend with 10  &micro;L  of DW.</li>
   <li>Suspend with 10  &micro;L  of DW.</li>
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<ol>
<ol>
   <li>Add 500  &micro;L  of GP1 to (~300 mg of) migrate gel and vortex.</li>
   <li>Add 500  &micro;L  of GP1 to (~300 mg of) migrate gel and vortex.</li>
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   <li>Incubate the mixture at 55C for (10~15) min and inverted it.</li>
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   <li>Incubate the mixture at 55&#8451; for (10~15) min and inverted it.</li>
   <li>Load the sample onto the column.</li>
   <li>Load the sample onto the column.</li>
   <li>Centrifuge at 13,000 rpm for 1 min.</li>
   <li>Centrifuge at 13,000 rpm for 1 min.</li>
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</table>
</table>
<p>Thermal protocol is following</p>
<p>Thermal protocol is following</p>
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<h3>2STEP Cycle (Tm value ≥ 63C)</h3>
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<h3>2STEP Cycle (Tm value ≥ 63&#8451;)</h3>
<table>
<table>
   <tr>
   <tr>
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Cycle: sequence2~3 &times; (25~45)
Cycle: sequence2~3 &times; (25~45)
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<h3>3STEP Cycle (Tm value ≤ 63C)</h3>
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<h3>3STEP Cycle (Tm value ≤ 63&#8451;)</h3>
<table>
<table>
   <tr>
   <tr>
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<ol>
<ol>
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  <li>Centrifuge 1 mL of culture at 8,000 rpm / for 2 min / at 4 C.</li>
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  <li>Centrifuge 1 mL of culture at 8,000 rpm / for 2 min / at 4&#8451;.</li>
  <li>Remove the supernatant.</li>
  <li>Remove the supernatant.</li>
  <li>Add 1 mL 0.15 M NaCl.</li>
  <li>Add 1 mL 0.15 M NaCl.</li>
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  <li>Centrifuge at 8,000 rpm / for 2 min / at 4 C.</li>
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  <li>Centrifuge at 8,000 rpm / for 2 min / at 4&#8451;.</li>
  <li>Remove the supernatant.</li>
  <li>Remove the supernatant.</li>
  <li>Add 350 &micro;L RLT and voltex it.</li>
  <li>Add 350 &micro;L RLT and voltex it.</li>
  <li>Add 350 &micro;L 70 % EtOH.</li>
  <li>Add 350 &micro;L 70 % EtOH.</li>
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  <li>Put 700 &micro;L of lysate on to column then centrifuge at 9,100 rpm / for 1 min / at 25 &deg;C.
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  <li>Put 700 &micro;L of lysate on to column then centrifuge at 9,100 rpm / for 1 min / at 25&deg;C.
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  <li>Remove filtrate and add 700 &micro;L RW1 then centrifuge at 9,100 rpm / for 1 min / at 25 &deg;C.</li>
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  <li>Remove filtrate and add 700 &micro;L RW1 then centrifuge at 9,100 rpm / for 1 min / at 25&deg;C.</li>
  <li>Remove filtrate and add 500 &micro;L RPE and centrifuge two times.</li>
  <li>Remove filtrate and add 500 &micro;L RPE and centrifuge two times.</li>
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  <li>Remove filtrate and centrifuge at 15,000 rpm / for 1 min / at 25 C.</li>
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  <li>Remove filtrate and centrifuge at 15,000 rpm / for 1 min / at 25&#8451;.</li>
  <li>Put the column on a new tube then add 30 &micro;L RNase free DW.</li>
  <li>Put the column on a new tube then add 30 &micro;L RNase free DW.</li>
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Latest revision as of 15:23, 9 September 2015

Notebook
Protocols

Protocols

Transformation

  1. Add (1~5) µL of (DNA) to (50) µL of thawed competent cells on ice.
  2. Incubate on ice for 30 min.
  3. Add (600) µL of LB.
  4. (Incubate the cells for 2 hrs at 37℃.)
  5. Spread 300 µL of the culture onto plate with LB and appropriate antibiotics.
  6. (Add 900 µL of LB to 100 µL of the culture and spread 300 µL of it onto second plate.)
  7. Incubate the plate(s) at 37℃ for 16~20 hours.

Mini-prep

Use FastGeneTM Plasmid mini kit (Nippon Genetics Co.,Ltd). This kit contains these reagents and wares: mP1 (resuspension buffer), mP2 (lysis buffer), mP3 (neutralization buffer), mP4 (first membrane wash buffer), mP5(second membrane wash buffer), mP6(elution buffer), column and collection tube.

  1. Centrifuge (1~5) mL of culture at (over 10,000) rpm for 2 min.
  2. Remove the supernatant.
  3. Add 200 µL of mP1 and voltex it.
  4. Add 200 µL of mP2 and invert the tube then leave it for 2 min at room temperature.
  5. Add 300 µL of mP3 then invert the tube.
  6. Centrifuge at 13,000 rpm for 2 min.
  7. Load the supernatant to column tube.
  8. Centrifuge at 13,000 rpm for 1 min.
  9. Remove filtrate and add 400 µL of mP4 then centrifuge 13,000 rpm for 1 min.
  10. Remove filtrate and add 600 µL of mP5 then centrifuge 13,000 rpm for 1 min.
  11. Remove filtrate and centrifuge 13,000 rpm for 2 min.
  12. Set column into 1.5 mL tube and add 50 µL of mP6.
  13. Centrifuge at 13,000 rpm for 2 min.

Ethanol precipitation

  1. Add (5) µL of NaOAc, 1.5 µL of glycogen and (125) µL of 100% ethanol.
  2. (Leave it at -80℃ for 1 hr. / Soak liquid nitrogen in an instant.)
  3. Centrifuge at 15,000 rpm for (10~15) min at 4℃.
  4. Remove supernatant and add (220) µL of 70% ethanol.
  5. Centrifuge at 15,000 rpm for (5~15) min at 4℃.
  6. Remove supernatant and air-dry at room temperature with light sheilding.
  7. Suspend with 10 µL of DW.

Ligation

Mix the following reagents in 0.2 mL PCR tube. Use DNA Ligation Kit Mighty Mix (Takara Bio Inc.) which contains ligase and buffer.

SolutionVector DNAInsert DNADWMighty MixTotal
Volume (µL)122510

Thermal protocol is following

SequenceTemp. (°C)Time (min)
11630
26510
34Hold

Digestion

Mix the following reagents in PCR tube.
Solution DNA RE1 10U/µL RE2 10U/µL Appropriate buffer Total
Volume (µL) 16 1 1 2 20
SequenceTemp. (°C)Time (min)
137120
26515
34Hold

Electrophoresis

  1. Put gel into electrophoresis tank.
  2. Pore 2x TBE buffer into the tank to soak gel.
  3. Add 5 µL of EtBr into cathod.
  4. Pre-migration for 30 min at 100 V.
  5. Apply DNA solution with 6x loading dye and ladder.
  6. Start electrophoresis at 100 V.

Gel extraction

Use FastGeneTM Gel/PCR Extraction kit (Nippon Genetics Co.,Ltd). This kit contains these reagents and wares: GP1 (binding buffer), GP2 (wash buffer), GP3 (elution buffer), column and collection tube.

  1. Add 500 µL of GP1 to (~300 mg of) migrate gel and vortex.
  2. Incubate the mixture at 55℃ for (10~15) min and inverted it.
  3. Load the sample onto the column.
  4. Centrifuge at 13,000 rpm for 1 min.
  5. Remove filtrate and add 600 µL of GP2 and centrifuge at 13,000 rpm for 1 min.
  6. Repeat step 5.
  7. Remove filtrate and centrifuge at 13,000 rpm for 2 min.
  8. Set column into 1.5 mL tube and add 50 µL of GP6.
  9. Centrifuge at 13,000 rpm for 2 min.

PCR

Use KOD -Plus- Neo (TOYOBO CO.,LTD) as polymerase. Mix PCR solutions and run the PCR machine in a program which is detailed below.

Solution template DNA Primer-F 10µM Primer-R 10µM MgSO4 dNTPs 10x Buffer KOD Plus Neo DW Total
Volume (µL) 1 1 1 3 5 5 1 33 50

Thermal protocol is following

2STEP Cycle (Tm value ≥ 63℃)

SequenceTemp. (°C)Time (sec)
194120
29810
36830sec / 1kbp
44Hold
Cycle: sequence2~3 × (25~45)

3STEP Cycle (Tm value ≤ 63℃)

SequenceTemp. (°C)Time (sec)
194120
29810
3Tm30
46830sec / 1kbp
54Hold
Cycle: sequence2~4 × (25~45)

Sequencing

Solution 5 x Sequencing Buffer primer 1µL template DNA Ready Reaction Premix DW Total
Volume (µL) 1.5 1.5 1 1 5 10
SequenceTemp. (°C)Time (sec)
19610
2505
360240
44Hold
Cycle: sequence2~4 × 25

Ethanol precipitation

Solution PCR product DW 3M NaOAc Glycogen 100% EtOH
Volume (µL) 10 10 2 1 50
  1. centrifuge at 15,000 rpm for 15 min at room temprature
  2. Remove supernatant ,add 100 µL of 70% EtOH and tap tubes by finger.
  3. centrifuge at 15,000 rpm for 10 min at room temprature
  4. Remove supernatant and air dry at room temperature, after that 10 µL of  DW is added and dissolve the precipitate.
  5. Electrophoresis
  6. Resuspend the pellet to HiDi formamide and remove to 96-well plate.
  7. Set the plate and start electrophoresis.

Streaking (Single colony isolation)

  1. Pick the colony with an inoculating loop from the agar plate.
  2. Drag the loop across on a new agar plate.
  3. Re-sterilise the loop and drag it across again.
  4. Repeat method 3.

Colony PCR

Solution DNA Kapa-Taq (Taq polymerase) EX-F primer 10µM PS-R primer 10µM DW Total
Volume (µL) 4 10 0.8 0.8 8.4 20
SequenceTemp. (°C)Time (sec)
195120
29530
368.930
47260
572120
64Hold
cycles: sequence2~4 × 30~45

RT-PCR

Purification of RNA from cell

Use RNeasy Mini Kit (QIAGEN). This kit contains these reagents and wares: RLT (lysis buffer), RW1(wash buffer), RPE(wash buffer), column and collection tube.

  1. Centrifuge 1 mL of culture at 8,000 rpm / for 2 min / at 4℃.
  2. Remove the supernatant.
  3. Add 1 mL 0.15 M NaCl.
  4. Centrifuge at 8,000 rpm / for 2 min / at 4℃.
  5. Remove the supernatant.
  6. Add 350 µL RLT and voltex it.
  7. Add 350 µL 70 % EtOH.
  8. Put 700 µL of lysate on to column then centrifuge at 9,100 rpm / for 1 min / at 25°C.
  9. Remove filtrate and add 700 µL RW1 then centrifuge at 9,100 rpm / for 1 min / at 25°C.
  10. Remove filtrate and add 500 µL RPE and centrifuge two times.
  11. Remove filtrate and centrifuge at 15,000 rpm / for 1 min / at 25℃.
  12. Put the column on a new tube then add 30 µL RNase free DW.
  13. Synthesizing cDNA

    Mix the following reagents in 0.2 mL PCR tube. Use SuperScript® VILOTM MasterMix (Life Technologies) which contains reverse transcriptase and buffer.

    SolutionMasterMixRNATotal
    Volume (µL)41620

    Thermal protocol is following

    SequenceTemp. (°C)Time (min)
    12510
    24260
    3855
    4-20Hold

    RT-PCR

    Mix the following reagents in 0.2 mL PCR tube. Use SYBR®GreenERTM qPCR SuperMix for ABI PRISM® (Life Technologies) which contains Taq DNA polymerase and buffer.

    SolutionSuperMixForward primerReverse primerTemplate cDNADEPC-treated water
    Volume (µL)12.50.50.5110.5

    Thermal protocol is following

    SequenceTemp. (°C)Time (min)
    1502
    29510
    3951/4
    4601

    cycles: sequence3-4 × 40