Endy:Screening plasmid/Inverter characterization/Protocols: Difference between revisions
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==Background== | ==Background== | ||
The inverters should be present in one of the [[Endy:PoPS based screening plasmid|PoPS based screening | The inverters should be present in one of the [[Endy:PoPS based screening plasmid|PoPS based screening plasmids]], this protocol refers to characterization of terminators in BBa_I13534 in CW2553+pJat8. pJat8 provides Gen resistance and the screening plasmid has Amp resistance. | ||
plasmids]], this protocol refers to characterization of terminators in BBa_I13534 in CW2553+pJat8. | |||
pJat8 provides Gen resistance and the screening plasmid has Amp resistance. | |||
The current characterization protocol follows the following steps: | The current characterization protocol follows the following steps: | ||
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==Procedure== | ==Procedure== | ||
Each culture has a different growth rate, so ensuring that the intermediate dilution and experimental | Each culture has a different growth rate, so ensuring that the intermediate dilution and experimental culture remain in log phase can be difficult. Additionally, the final culture must match induction time (so that the fluorophore concentration reaches steady state) and growth time (so that the culture is dense enough to measure at the end of the experiment, but still in mid-log). Rough guidelines for timing are included below. | ||
culture remain in log phase can be difficult. Additionally, the final culture must match induction | |||
time (so that the fluorophore concentration reaches steady state) and growth time (so that the culture | |||
is dense enough to measure at the end of the experiment, but still in mid-log). Rough guidelines for | |||
timing are included below. | |||
===Day 1=== | ===Day 1=== | ||
====Set up Overnights==== | ====Set up Overnights==== | ||
It is only necessary to set up one 5ml overnight culture per experiment device (inverter) or control. | It is only necessary to set up one 5ml overnight culture per experiment device (inverter) or control. These cells typically grow very slowly. I set up overnights early in the afternoon in a richer media (M9/glucose works reasonably well) and give them plenty of time to grow up. | ||
These cells typically grow very slowly. I set up overnights early in the afternoon in a richer media | |||
(M9/glucose works reasonably well) and give them plenty of time to grow up. | |||
*Controls | *Controls | ||
**Negative Control - CW2553/pJat8 | **Negative Control - CW2553/pJat8 | ||
| Line 48: | Line 32: | ||
===Day 2=== | ===Day 2=== | ||
====Dilute back in AM==== | ====Dilute back in AM==== | ||
For high copy plasmids, I estimate a doubling time of 1.5 to 2 hours. I generally dilute back 100x | For high copy plasmids, I estimate a doubling time of 1.5 to 2 hours. I generally dilute back 100x into 5ml of M9/glycerol and grow for 8-10 hours. For low copy plasmids, either shorten the growth time (5-6 hours rather than 8-10) or increase the dilution. | ||
into 5ml of M9/glycerol and grow for 8-10 hours. For low copy plasmids, either shorten the growth time | |||
(5-6 hours rather than 8-10) or increase the dilution. | |||
====Set up overnight experimental cultures==== | ====Set up overnight experimental cultures==== | ||
A 12 hours induction seems to provide sufficient time for the fluorophores to reach steady state | A 12 hours induction seems to provide sufficient time for the fluorophores to reach steady state (previous results with an empty screening plasmid have shown unchanged levels between 12 and 14 hours). For a high copy plasmid, innoculating at OD 0.002 works reasonably well. Lower copy plasmids will need smaller innoculums (OD 0.0001-0.0005). | ||
(previous results with an empty screening plasmid have shown unchanged levels between 12 and 14 | |||
hours). For a high copy plasmid, innoculating at OD 0.002 works reasonably well. Lower copy plasmids | |||
will need smaller innoculums (OD 0.0001-0.0005). | |||
concentrations + 2) * #replicates | In previous experiments, we used 6-8 arabinose induction levels to test inverters, ranging from 0%-0.003%. We have usually induced our cultures with 0%, 10<sup>-6</sup>%, 3*10<sup>-6</sup>%, 10<sup>-5</sup>5%, 3*10<sup>-5</sup>%, 10<sup>-4</sup>%, 3*10<sup>-4</sup>%, 10<sup>-3</sup>%, and 3*10<sup>-3</sup>% arabinose. It is usually a good idea to make up large batches of media + arabinose and then make 5ml aliquots of this for each experimental device -- this ensures they all see the same levels of arabinose. Each experimental strain as well as the empty plasmid control should be innoculated in all of the arabinose concentrations, the negative control can be grown with no arabinose, and the GFP only control should be grown in 0.003% to maximize the FL output. So total samples will be ((EXP+1)*#arab concentrations + 2) * #replicates | ||
===Day 3=== | ===Day 3=== | ||
| Line 86: | Line 44: | ||
====Run samples on FACS==== | ====Run samples on FACS==== | ||
#Set PMT voltages based on the Empty plasmid control. The GFP and RFP signals should both be centered | #Set PMT voltages based on the Empty plasmid control. The GFP and RFP signals should both be centered around 100 FLunits. | ||
around 100 FLunits. | |||
#The droplet maker can be turned off to reduce noise in the signal if you are not sorting the cells. | #The droplet maker can be turned off to reduce noise in the signal if you are not sorting the cells. | ||
#Run beads (~6 drops in ) - this is used to verify that the lasers are aligned as well as to serve as | #Run beads (~6 drops in ) - this is used to verify that the lasers are aligned as well as to serve as a calibration between runs, you can read more about his in the [[Endy:Terminator characterization/Analysis|analysis techniques]]. | ||
a calibration between runs, you can read more about his in the [[Endy:Terminator | |||
characterization/Analysis|analysis techniques]]. | |||
#*ADD HERE an example of what peaks should look like if setting are good and laser is aligned. | #*ADD HERE an example of what peaks should look like if setting are good and laser is aligned. | ||
#Run the empty plasmid again, followed by the negative control. | #Run the empty plasmid again, followed by the negative control. | ||
#*This allows you to determine the "noise region", since you shouldn't trust readings that are within | #*This allows you to determine the "noise region", since you shouldn't trust readings that are within the range of autoflourescence of your cells. Also, it makes sure that the method being used to clear the tubing between samples is working well. If you still see many positive cells in the negative control then you can try running bleach between samples. (This is maybe more important between different terminators then between different arabinose concentrations). | ||
the range of autoflourescence of your cells. Also, it makes sure that the method being used to clear | |||
the tubing between samples is working well. If you still see many positive cells in the negative | |||
control then you can try running bleach between samples. (This is maybe more important between | |||
different terminators then between different arabinose concentrations). | |||
#Run the experimental samples. | #Run the experimental samples. | ||
==Analysis== | ==Analysis== | ||
Revision as of 19:21, 16 February 2006
This is a work in progress, protocol is currently incomplete
Purpose
Characterize the invivo transfer function of a Biobricked inverter quickly and reliably.
Background
The inverters should be present in one of the PoPS based screening plasmids, this protocol refers to characterization of terminators in BBa_I13534 in CW2553+pJat8. pJat8 provides Gen resistance and the screening plasmid has Amp resistance.
The current characterization protocol follows the following steps:
Day 1:
- Grow the cells overnight in a rich media to achieve density.
Day 2:
- Dilute back to return the cells to mid-log in M9/gly
- Innoculate experimental cultures of M9/gly/ara
Day 3:
- Harvest cells for FACS
- Run FACS
Procedure
Each culture has a different growth rate, so ensuring that the intermediate dilution and experimental culture remain in log phase can be difficult. Additionally, the final culture must match induction time (so that the fluorophore concentration reaches steady state) and growth time (so that the culture is dense enough to measure at the end of the experiment, but still in mid-log). Rough guidelines for timing are included below.
Day 1
Set up Overnights
It is only necessary to set up one 5ml overnight culture per experiment device (inverter) or control. These cells typically grow very slowly. I set up overnights early in the afternoon in a richer media (M9/glucose works reasonably well) and give them plenty of time to grow up.
- Controls
- Negative Control - CW2553/pJat8
- Empty Plasmid - This provides a baseline for calibrating GFP and RFP
- GFP only - This enables quantification of bleed from GFP in RFP filter
- (We have these results should link to the measurements here.)
Day 2
Dilute back in AM
For high copy plasmids, I estimate a doubling time of 1.5 to 2 hours. I generally dilute back 100x into 5ml of M9/glycerol and grow for 8-10 hours. For low copy plasmids, either shorten the growth time (5-6 hours rather than 8-10) or increase the dilution.
Set up overnight experimental cultures
A 12 hours induction seems to provide sufficient time for the fluorophores to reach steady state (previous results with an empty screening plasmid have shown unchanged levels between 12 and 14 hours). For a high copy plasmid, innoculating at OD 0.002 works reasonably well. Lower copy plasmids will need smaller innoculums (OD 0.0001-0.0005).
In previous experiments, we used 6-8 arabinose induction levels to test inverters, ranging from 0%-0.003%. We have usually induced our cultures with 0%, 10-6%, 3*10-6%, 10-55%, 3*10-5%, 10-4%, 3*10-4%, 10-3%, and 3*10-3% arabinose. It is usually a good idea to make up large batches of media + arabinose and then make 5ml aliquots of this for each experimental device -- this ensures they all see the same levels of arabinose. Each experimental strain as well as the empty plasmid control should be innoculated in all of the arabinose concentrations, the negative control can be grown with no arabinose, and the GFP only control should be grown in 0.003% to maximize the FL output. So total samples will be ((EXP+1)*#arab concentrations + 2) * #replicates
Day 3
Prepare FACS Samples
Take 1 ml aliquots and place on ice.
Run samples on FACS
- Set PMT voltages based on the Empty plasmid control. The GFP and RFP signals should both be centered around 100 FLunits.
- The droplet maker can be turned off to reduce noise in the signal if you are not sorting the cells.
- Run beads (~6 drops in ) - this is used to verify that the lasers are aligned as well as to serve as a calibration between runs, you can read more about his in the analysis techniques.
- ADD HERE an example of what peaks should look like if setting are good and laser is aligned.
- Run the empty plasmid again, followed by the negative control.
- This allows you to determine the "noise region", since you shouldn't trust readings that are within the range of autoflourescence of your cells. Also, it makes sure that the method being used to clear the tubing between samples is working well. If you still see many positive cells in the negative control then you can try running bleach between samples. (This is maybe more important between different terminators then between different arabinose concentrations).
- Run the experimental samples.
Analysis
...
Contact
- protocol based on screening plasmid protocols developed by
