Team:MIT/InterlabStudy


Introduction
The iGEM Interlab Study's aim is "to obtain fluorescence data for three specific genetic devices expressing GFP from iGEM teams around the world”. It is an opportunity for teams throughout the world to build and characterize parts. The purpose of the study as a whole is to be able to “test the consistency of the teams’ data of the measured devices”.
Devices Built and Measured: (Chassis : E coli)
Device 1 : J23101 + I13504 (B0034-E0040-B0015) -> backbone:PSB1C3 (3 biological replicates)
Device 2 : J23106 + I13504 (B0034-E0040-B0015) -> backbone:PSB1C3 (3 biological replicates)
Device 3 : J23117 + I13504 (B0034-E0040-B0015) -> backbone: PSB1C3 (3 biological replicates)
Measurement Controls:
Positive Control: I20270 PSB1C3 -> J23151 + I20270(B0032-E0040-B0010-B0012)
Negative Control: BBa_R0040
Negative Control : NEB 10 B Competent Cells
Protocols:
DNA Kit Plate Instructions (http://parts.igem.org/Help:2015_DNA_Distribution)
Transformation (http://parts.igem.org/Help:Protocols/Transformation)
Making Liquid cultures:
• Prepare culture in a 15 mL, round bottom tube.
• Add 5mL LB using a seriological pipette
• Add 5uL of 1000x antibiotic (Chloramphenicol.)
• Pick colony using a 10 ul pipette tip on a p2. Eject tip into tube (tip should remain in tube).
• if growing from another liquid culture, 100 uL should be plenty (replacing the 1 colony). Almost no amount is too small, just ensure that you get cells.
Miniprep – using Qiagen protocol
3 Antibiotic Assembly protocol
Transformation
Colony PCR (selecting transformants from the transformation plates)
Making Liquid Culture (see above)

Generalized E coli Flow Cytometry Protocol( created by Nicholas Delateur Weiss Lab MIT)
  1. Grow an overnight in rich media with appropriate antibiotic from a single colony (in previous step)
  2. Subculture 125 uL of saturated culture into 5 mL of M9 Minimal Media (below) supplemented with Glycerol, add appropriate antibiotic
  3. Grow with shaking at desired temperature until desired OD (0.3 for exponential phase, 1.0ish for steady phase)
  4. Dilute 10 uL into 990 uL 1X PBS
  5. Interrogate by flow cytometry

M9 Min w/ Glycerol Recipe

  • 20 mL 5X m9
  • 3.4 mL 10mg/mL thiamine
  • 0.8 mL 50% glycerol
  • 2 mL 10% cas AA
  • 0.2 mL  1 M MgSO4
  • 10 uL 1 M CaCl2
Mix, and then add DI water until the total volume is 100 mL (for a total of 100 mL)
Measuring in flow cytometer
  1. measured beads
  2. measured 3 types of devices
  3. measured positive control : I20270 (GFP construct)
  4. measure negative controls : Untransformed competent cell and R0040
Sequencing
Final Data
Results

Flow Cytometer Data

Graphs

J23101+ GFP

J23106 + GFP

J23117 + GFP

Conclusions
This iGEM Interlab Study yielded results that are in alignment with the 2006 UC Berkeley "Anderson Promoter" Study(which measured RFP fluorescence). Our study proved that among the 3 promoters (J23101, J23106, J23117), the J23101 Promoter was the strongest as it had the highest GFP fluorescence associated with it. In order of strength, the J23101 Promoter was the highest, the J23106 Promoter was moderate (in the middle), and the J23117 Promoter was the lowest.