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Team:DTU-Denmark/Interlab form
From 2014.igem.org
iGEM 2014 Measurement Interlab Study Worksheet<o:p></o:p>
To participate in this study, please complete the following worksheet and submit to measurement [AT] igem [DOT] org.<o:p></o:p>
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Inter-Lab Study Worksheet:<o:p></o:p>
For each assay that you perform, fill out the following worksheet. Answer each question with enough detail to allow another person to replicate your measurements without needing to ask you any questions. This does not necessarily mean you need to describe everything in detail---for example, if you use a standard assay, you just need to give enough information to allow another person to use that assay in the same way that you did.<o:p></o:p>
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Section I: Provenance & Release<o:p></o:p>
<![if !supportLists]>1. <![endif]>Who did the actual work to acquire these measurements?<o:p></o:p>
Our laboratory group carried out the experiments this group consists of Anne Sofie Lærke Hansen, Anne Pihl Bali, Caroline Mosbech, Kristian Barreth Karlsen, Kristian Jensen & Rasmus Bech<o:p></o:p>
<![if !supportLists]>2. <![endif]>What other people should be credited for these measurements? (i.e., who would be an author on any resulting publication. For example, your faculty advisor may have helped design the protocols that you ran.)<o:p></o:p>
We did all the experiments for the interlab study ourselves…<o:p></o:p>
Ali Altintas assisted us in setting up the BioLector. Anne Egholm helped us to use the Flow Cytometer.<o:p></o:p>
<![if !supportLists]>3. <![endif]>On what dates were the protocols run and the measurements taken? (this will often be a range of dates; make sure you say which data was taken at what times.)<o:p></o:p>
BioLector was running: 10th-11th of September 2014<o:p></o:p>
Flow cytometry was done on the 22nd of September. <o:p></o:p>
<![if !supportLists]>4. <![endif]>Do all persons involved consent to the inclusion of this data in publications derived from the iGEM interlab study?<o:p></o:p>
Yes.<o:p></o:p>
Section II: Protocol<o:p></o:p>
<![if !supportLists]>1. <![endif]>What protocol did you use to prepare samples for measurement?<o:p></o:p>
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Construct strains: <o:p></o:p>
Create multiple strains expressing GFP from different promoters from the Andersen Library. Constructs were prepared with Standard Assembly. (see protocol). <o:p></o:p>
Plasmid were purified with Zyppy™ Plasmid Miniprep Kit from Zymo research. Followed manufacturer's protocol. <o:p></o:p>
Competent DH5α cells were prepared (see protocol).<o:p></o:p>
Purified plasmids were transformed into competent DH5α cells. <o:p></o:p>
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Culture measurements:<o:p></o:p>
We used cell culture tubes (10 mL) containing 2 mL LB medium (with 0.5% NaCl) and 25 μg/mL chloramphenicol for each strain. To each of the tubes, we inoculated cells from a single colony with a sterile inoculation loop and left it overnight at 37°C, shaking at 350 rpm. <o:p></o:p>
The wells of the sterile BioLector plate (48 well FlowerPlate) was prepared with 1450 μL (1500μL for controls) of LB (0.5% NaCl) containing 25 μg/mL chloramphenicol. The following day we transferred 10 μL of each culture into an Eppendorf tube with 990 μL of sterile physiological salt water (creating a 100-fold dilution). We inoculated the individual BioLector wells with 10 μL of the dilution (creating an additional 150-fold dilution). Each strain was grown in triplicates to make sure we had 3 independent measurements and a more precise result. We incubated the plate in the BioLector at 37°C and 1000 rpm for 12.5 hours (stationary phase was reached). During the growth experiment we measured biomass and GFP fluorescence every 5 minutes. Biomass was measured by light scatter at 620 nm, while fluorescence was measured at 520 nm, with an excitation wavelength of 488 nm.<o:p></o:p>
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Single cell measurements:<o:p></o:p>
2 mL LB (0.5% NaCl) was inoculated with cells from a plate and grown overnight.<o:p></o:p>
The cultures were washed and resuspended in PBS.<o:p></o:p>
The cell suspensions were diluted in PBS to a concentration where the flow cytometer could detect 1000-1500 events per second.<o:p></o:p>
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<![if !supportLists]>2. <![endif]>What sort of instrument did you use to acquire measurements?<o:p></o:p>
<![if !supportLists]>§ <![endif]>What is the model and manufacturer? <o:p></o:p>
Instrument: BioLector® (Basic) - Microbioreactor System <o:p></o:p>
Manufacturer: m2p-laps<o:p></o:p>
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Instrument: FACSCalibur Cell Analyzer<o:p></o:p>
Manufacturer: BD Biosciences<o:p></o:p>
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<![if !supportLists]>§ <![endif]>How is it configured for your measurements? (e.g., light filters, illumination, amplification)<o:p></o:p>
The BioLector is fitted with filters for measuring biomass (scatter at 620 nm) and GFP (emission at 520 nm, excitation with 488 nm). <o:p></o:p>
GAIN: <o:p></o:p>
GFP: 80 <o:p></o:p>
Biomass: 30<o:p></o:p>
Humidity was controlled at 95%.<o:p></o:p>
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The FACSCalibur was used with settings…<o:p></o:p>
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<![if !supportLists]>3. <![endif]>What protocol did you use to take measurements?<o:p></o:p>
The BioLector was instructed to take measurements every 5 minutes.<o:p></o:p>
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The FACS was set up with a threshold on side scatter, as events with low side-scatter are very likely noise, i.e. not actual cells. Each sample was then analysed at 1000-1500 events per second, until a total of 100,000 events was reached.<o:p></o:p>
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<![if !supportLists]>4. <![endif]>What method is used to determine whether to include or exclude each sample from the data set?<o:p></o:p>
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Strains that showed correct digest patterns were included. Strains that were sequenced and showed wrong sequences were excluded. As were cultures that did not grow, and single replicates that showed negligible fluorescence. <o:p></o:p>
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<![if !supportLists]>5.
<![endif]>What exactly
were the controls that you used?
DH5α with BBa_E0240 (no promoter) was used
to determine cell background fluorescence (without GFP). For the BioLector, clean media was used to determine media
fluorescence.<o:p></o:p>
<![if !supportLists]>6.
<![endif]>What quantities
were measured? (e.g., red fluorescence, green fluorescence, optical density)
On the BioLector: GFP
fluorescence (488 nm /520 nm) and biomass (scatter at 620nm). The flow
cytometer measured forward scatter (cell size), side scatter (cell granularity)
and fluorescence.<o:p></o:p>
<![if !supportLists]>7.
<![endif]>How much time
did it take to acquire each set of measurements?
The running time of the BioLector
experiment was 12 hours and 30 minutes. <o:p></o:p>
One cycle: 4.86 min. <o:p></o:p>
Flow cytometry: The measurements themselves took less than 1 hour.<o:p></o:p>
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<![if !supportLists]>8. <![endif]>How much does it cost to acquire a set of measurements?<o:p></o:p>
Assuming the lab already
have a BioLector..
For a full plate with
samples: Flowerplate for the BioLector,
170mL LB medium, chloramphenicol, 16 pts. inoculation
tubes, tips, Eppendorf tubes approximately $100.<o:p></o:p>
<![if !supportLists]>9.
<![endif]>What are the
practical limits on the number or rate of measurements taken with this instrument
and protocol?
BioLector: With the used
protocol 48 samples can be measured within short intervals of time, however, 3
of these should be used as control. So when measuring triplicates it is
possible to measure 15 different strains in the protocol used for the interlab study. Analysing such
a plate takes approximately 24 hours.<o:p></o:p>
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Section III: Measured Quantities<o:p></o:p>
<![if !supportLists]>1. <![endif]>For each type of quantity measured (e.g., fluorescence, optical density), report on the following:<o:p></o:p>
<![if !supportLists]>2. <![endif]>Units:<o:p></o:p>
<![if !supportLists]>§ <![endif]>What are the units of the measurement? (e.g., meters, molecules)<o:p></o:p>
All measurements are in arbitrary units.<o:p></o:p>
<![if !supportLists]>§ <![endif]>What is the equivalent unit expressed as a combination of the seven SI base units? (<a href="http://en.wikipedia.org/wiki/SI_base_unit">http://en.wikipedia.org/wiki/SI_base_unit</a>)<o:p></o:p>
Not applicable.<o:p></o:p>
<![if !supportLists]>3. <![endif]>Precision:<o:p></o:p>
<![if !supportLists]>§ <![endif]>What is the range of possible measured values for this quantity, using your instrument as configured for these measurements? (e.g., a meter stick measures in the range of 0 to 1 meter)<o:p></o:p>
Linear range for
OD 600 is between 0.2 and 600.
Linear range for GFP XXXXX<o:p></o:p>
<![if !supportLists]>§ <![endif]>What are the significant figures for these measurement?
(e.g., on a meter stick, it is common to measure to the nearest millimeter).
We have estimated a mixed model with promoter as fixed
effect and replicates as random effects, this model showed the residual
standard deviation as 0.040. With this result we can say that a single
measurement is no more precise than the measured value ± 0.040.<o:p></o:p>
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<![if !supportLists]>§
<![endif]>Is the precision
the same across the entire range? If not, how does it differ?
Presumeably<o:p></o:p>
<![if !supportLists]>§ <![endif]>How did you determine these answers?<o:p></o:p>
<![if !supportLists]>2. <![endif]>Accuracy:<o:p></o:p>
<![if !supportLists]>§ <![endif]>When was the instrument last calibrated?<o:p></o:p>
approximately 5 years old machine. Filters changed 3 years ago. <o:p></o:p>
self calibration every cycle. <o:p></o:p>
<![if !supportLists]>§ <![endif]>How was the instrument calibrated?<o:p></o:p>
Section IV: Measurements<o:p></o:p>
<![if !supportLists]>1. <![endif]>For each sample, report:<o:p></o:p>
<![if !supportLists]>§ <![endif]>the identity of the sample<o:p></o:p>
<![if !supportLists]>§ <![endif]>each quantity directly measured<o:p></o:p>
<![if !supportLists]>§ <![endif]>each quantity derived from measurements (e.g., fluorescence/OD)<o:p></o:p>
<![if !supportLists]>2. <![endif]>For each group of replicates, report:<o:p></o:p>
<![if !supportLists]>§ <![endif]>the identity of samples in the set<o:p></o:p>
<![if !supportLists]>§ <![endif]>which, if any, of the samples are excluded and why<o:p></o:p>
In two of the triplicate sets, one outlier was excluded: For the promoter J23100, one replicate did not grow. For promoter J23102 one replicate had negligible fluorescence.<o:p></o:p>
<![if !supportLists]>§ <![endif]>the mean and standard deviation for each quantity measured or derived<o:p></o:p>
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