Team:Cornell/Notebook/Salicylate reporter

From 2012.igem.org

(Difference between revisions)
(July 1st, Monday)
(June: got rid of week sections)
Line 5: Line 5:
==June==
==June==
-
===Week===
+
===June 29th, Friday===
-
====June 29th, Friday====
+
* [[Vent PCR]] at 11:00 (DPW)
* [[Vent PCR]] at 11:00 (DPW)
** Amplifying both previous Phusion PCR band and original p21 template
** Amplifying both previous Phusion PCR band and original p21 template
Line 33: Line 32:
** Appending BioBrick cutsites for ligation into pSB3C5
** Appending BioBrick cutsites for ligation into pSB3C5
<br>
<br>
-
====June 30th, Saturday====
+
===June 30th, Saturday===
* Took PCR out of thermal cycler at 9:00 am (DPW)
* Took PCR out of thermal cycler at 9:00 am (DPW)
** Set up gel using NEB 100bp and 2-log ladders (10:00am)
** Set up gel using NEB 100bp and 2-log ladders (10:00am)
Line 52: Line 51:
** Second transformation performed at [[Myers and Myers]] specification of 0.55 kV (time constant of 9.34 ms).
** Second transformation performed at [[Myers and Myers]] specification of 0.55 kV (time constant of 9.34 ms).
<br>
<br>
-
====July 1st, Sunday====
+
 
 +
==July==
 +
===July 1st, Sunday===
* Set up gel for electrophoresis (9:50am, DPW + CMR)
* Set up gel for electrophoresis (9:50am, DPW + CMR)
** 1% gel in BIO-RAD Mini-Sub Cell system for continuation of ladder test using SYBR Green(10:50, CMR)
** 1% gel in BIO-RAD Mini-Sub Cell system for continuation of ladder test using SYBR Green(10:50, CMR)
Line 66: Line 67:
<br>
<br>
Replated p21, p22, JG700, JG1220, JG1537, JG1219
Replated p21, p22, JG700, JG1220, JG1537, JG1219
-
===Week===
+
 
-
====July 2nd, Monday====
+
===July 2nd, Monday===
Today, Dylan and Caleb ran a [[Team:Cornell/DNA Gel Electrophoresis|gel]] of a [[Team:Cornell/Vent PCR|Vent PCR]] of p21 (the PCR product being the salicylate reporter), then [[Team:Cornell/Qiagen Gel Extraction|gel extracted]] the appropriately-sized fragment, and finally [[Team:Cornell/Double Digest|digested]] the gel extracted salicylate reporter with EcoRI and AscI.
Today, Dylan and Caleb ran a [[Team:Cornell/DNA Gel Electrophoresis|gel]] of a [[Team:Cornell/Vent PCR|Vent PCR]] of p21 (the PCR product being the salicylate reporter), then [[Team:Cornell/Qiagen Gel Extraction|gel extracted]] the appropriately-sized fragment, and finally [[Team:Cornell/Double Digest|digested]] the gel extracted salicylate reporter with EcoRI and AscI.

Revision as of 15:04, 2 July 2012

Home Team Project Parts Modeling Notebook Protocols Safety Attributions

Contents

Write description

June

June 29th, Friday

  • Vent PCR at 11:00 (DPW)
    • Amplifying both previous Phusion PCR band and original p21 template
    • Dylan's magic triple anneal method (55/60/63)
  • Gel purified PCR product from Phusion template (~1:20 pm) (DPW)
    • Quantified product at 22.4 ng/uL
    • Set up digestion of p21 PCR product with EcoRI-HF and AscI (~9:00 pm).
      • 22 ng/uL --> 45.5 uL sample for 1 ug digest
      • Buffer 4
    • Ran digestion on gel. (~11:00 pm)
    • Sliced out relevant band on gel, stored overnight at -20.


  • Miniprepped overnight cultures of PL14-PL20 (~1:00 pm, STC)
    • Using C1015 rotor, 6666 x g, the Corning culture tubes only fit in the centrifuge with the lids off


  • Made LB, 3x 60 mL in 100 mL bottles (~ 3:00pm, SS)
  • Made LB Agar, 4 x 250 mL LB Agar in 500 mL bottles (~3:00, CS)
  • Autoclaved LB, LB Agar, and milliQ (~3:30 pm, SS)
  • Made LB plates with Kan (~6:30 pm, CMR)


  • CUGEM movie outing at 8:00 pm.


  • Phusion PCR at 10:00 pm (DPW)
    • Dylan's magic triple anneal method (57/65/70, 35 cycles total)
    • Amplifying nah operon from Gibson 1
    • Appending BioBrick cutsites for ligation into pSB3C5


June 30th, Saturday

  • Took PCR out of thermal cycler at 9:00 am (DPW)
    • Set up gel using NEB 100bp and 2-log ladders (10:00am)
    • Gel extracted PCR product, quantified at ~10ng/uL
    • Set up new Phusion PCR using Gibson 1 as template
      • Dylan's magic three-anneal method (57.6/65/72)
      • Extension time of 3 min.


  • Continued gel extraction of p21 PCR digest from previous day (SS)
  • Set up ligation of p21 PCR digest extraction and dephosphorylated pBBRBB+mtrB (11:11am, SS)
    • Desalted ligation using Millipore membrane paper
    • Transformed 2 electrocompetent DH5alpha stocks at 5:30 pm and 5:50 pm, respectively.
    • Observed time constants for electroporation of 4.38 ms and 4.24 ms, respectively
    • Let cells recover for 1 hour, plated on LB + Kan.


  • Set up two ligations of pSB3C5 into PNNL electrocompetent Shewanella strain JG700 (6:30 pm, Sp.C and St.C)
    • First transformation performed at usual PNNL voltage of 0.75 kV (time constant of 9.30 ms)
    • Second transformation performed at Myers and Myers specification of 0.55 kV (time constant of 9.34 ms).


July

July 1st, Sunday

  • Set up gel for electrophoresis (9:50am, DPW + CMR)
    • 1% gel in BIO-RAD Mini-Sub Cell system for continuation of ladder test using SYBR Green(10:50, CMR)
      • Ran NEB 100 bp ladder, NEB 2-log ladder, Promega 1 kb ladder
      • Ran at 100 V.
    • 1% gel in Owl box using ethidium bromide (10:50, DPW)
      • Ran nah operon PCR product from previous night
      • Ran at 55 V.


Because we learned that our SYBR Green was causing ladder to run strangely, Dylan decided to redo a Vent PCR to amplify the salicylate reporter region out of p21.
Liquid culture of JG700.
Replated p21, p22, JG700, JG1220, JG1537, JG1219

July 2nd, Monday

Today, Dylan and Caleb ran a gel of a Vent PCR of p21 (the PCR product being the salicylate reporter), then gel extracted the appropriately-sized fragment, and finally digested the gel extracted salicylate reporter with EcoRI and AscI.