Team:Tokyo Tech/Experiment/Interlab
Interlab
contents
1. Introduction
2. Summary of the Experiment
3. Results
3.1. Plate reader
3.2. Flow cytometer
4. Materials and Methods
4.1. Construction
4.2. Instruments and Date
4.2.1. Instruments
4.2.2. Date
4.3. Protocol
4.3.1. Plate reader
4.3.2. Flow cytometer
4.4. How to process the data
4.4.1. Plate reader
4.4.2. Flow cytometer
4.5. Individuals responsible for conducting Interlab study
5. Reference
1. Introduction
In iGEM 2015, the Interlab Study was held, where we measured the expression level of GFP using three designated devices. It was the first time for our team to join this Interlab Study. In addition to the three designated devices, we also measured the expression level of GFP from a positive control and a negative control using the flow cytometer and the plate reader. Also, for the plate reader, we succeeded in calculating the absolute unit by drawing the calibration curve using sodium fluorescein.
2. Summary of the Experiment
Our purpose was to obtain the fluorescence data of the three designated devices and to compare them. We prepared Device1〜Device3, Positive control and Negative control as shown below. We measured the exact same colonies of the exact same samples with both the plate reader and the flow cytometer.
Device 1: J23101 + I13504(pSB1C3)
Device 2: J23106 + I13504(pSB1C3)
Device 3: J23117 + I13504(pSB1C3)
Positive control: BBa_I20270(pSB1C3)
Negative control: BBa_R0040(pSB1C3)
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Fig.3-6-2-1. designated devices |
3. Results
3.1. Plate reader
First of all, we calibrated our plate reader by confirming the linear relationship between sodium fluorescein concentration and fluorescence (Fig. 3-6-3-1). The way we obtained the calibration curve is descried in the 4. Material and Method section.
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Fig.3-6-3-1. Calibration curve |
We measured three colonies(#1〜3) three times (Technical replicate 1〜3) per each sample (Device1〜3, positive control and negative control).
Using the calibration curve (Fig. 3-6-3-1), we were able to obtain the absolute unit of fluorescence (Table. 3-6-3-1). The way we obtained the absolute unit is described in the 4. Material and Method section. These results show that the intensity of fluorescence was in the following order, Device1>Device2>positive control>Device3>negative control.
Table. 3-6-3-1. The absolute unit of fluorescence intensity | |
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We calculated the arithmetic mean for each sample by adding the nine values of all three colonies and dividing it by 9. We also calculated the standard deviation for each sample from the calculated arithmetic mean. (Table. 3-6-3-2)
Table. 3-6-3-2. Arithmetic mean (Mean) and Standard deviation (S.D) of samples. | |
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Fig.3-6-3-2. Results from the plate reader
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3.2. Flow cytometer
We measured the geometric mean of fluorescence intensity for each sample. The results are shown below (Table.3-6-3-3). We measured three colonies(#1〜3) three times (Technical replicate 1〜3) per each sample (Device1〜3,positive control and negative control).
These results show that the intensity of fluorescence was in the following order, Device1>Device2>positive control>Device3>negative control. (Table. 3-6-3-4)(Fig. 3-6-3-3)
These results are the same as the results from the measurement done by the plate reader.
Table. 3-6-3-3. Results from the flow cytometer | |
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Table. 3-6-3-4. Arithmetic mean (Mean) and Standard deviation (S.D) of samples. | |
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Fig.3-6-3-3. Results from the flow cytometer
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4. Materials and Methods
4.1. Construction
-Strain
All the samples were DH5alpha strain.
-Plasmids
Device 1: J23101 + I13504(pSB1C3)
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Fig.3-6-4-1. |
Device 2: J23106 + I13504(pSB1C3)
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Fig.3-6-4-2. |
Device 3: J23117 + I13504(pSB1C3)
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Fig.3-6-4-3. |
Positive control: BBa_I20270(pSB1C3)
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Fig.3-6-4-4. |
Negative control: BBa_R0040(pSB1C3)
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Fig.3-6-4-5. |
-Sequence Data
Please refer to Sequence Data page.
4.2. Instruments and Date
4.2.1. Instruments
-Plate reader
We used FujiFilm FLA-5100 Fluorescent Image Analyzer from FUJIFilm Life Science. The wavelength of light we used to excite the cells was 473 nm. We used BPB1 (530DF20) filter to capture the light emission from the cells. The sampling frequency is only one time.
-Flow cytometer
We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company. The wavelength of light we used to excite the cells was 488 nm. We used laser detection channel FL1 to capture the light emission from the cells. Laser detection channel Fl1 was used with sensitivity 680 [v]. The sampling frequency is only one time.
4.2.2. Date
Cloning of constructs was confirmed by August 21st 2015. Transformant plates were from 24 August 2015. All the samples were measured on August 27th 2015.
4.3. Protocol
4.3.1. Plate reader
1. Prepare 3 over night cultures for each sample Device1〜Device3, Positive control and Negative control in 3 mL LB medium containing chloramphenicol (35 microg / mL) at 37°C for 17 h and shake at 180 rpm.
2. Measured the OD590 of each sample and diluted each sample to adjust OD590 within 5% of 0.5.
3. Set the plate reader to measure GFP.
4. Take 1 mL of the samples, and centrifuge at 9000x g, 1 min, 4°C.
5. Remove the supernatants by using P1000 pipette.
6. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspended.
7. Place 200 microL of each sample into the 96-well plate as described in Table. 3-6-4-1.
8. Measure the fluorescence intensity with plate reader.
9. Rotate the 96-well plate 180 degrees horizontally and measure the fluorescence intensity again.
Table. 3-6-4-1. Position of samples in 96-well plate | |
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4.3.2. Flow cytometer
1. Prepare 3 over night cultures for each sample Device1〜Device3, Positive control and Negative control in 3 mL LB medium containing chloramphenicol (35 microg / mL) at 37°C for 17 h and shake at 180 rpm.
2. Start preparing the flow cytometer 1 h before the end of incubation.
3. Measure the OD590 and adjust the volume of each sample to centrifuge so that the amount of pellet will be about the same for every sample.
4. Centrifuge the samples at 9000x g, 1 min, 4°C.
5. Remove the supernatants by using P1000 pipette and suspend the samples with 1 mL of filtered PBS (phosphate-buffered saline).
6. Dispense all of each suspension into a disposable tube through a cell strainer.
7. Measure fluorescence intensity with flow cytometer.
4.4. How to process the data
4.4.1. Plate reader
-How to draw the calibration curve
1. Place 200 microL of various concentrations of sodium fluorescein (500, 375, 250, 125, 50, 25, 10, 5 ng / mL and PBS only) into the 96-well plate in triplicate.
2. Measure the fluorescence intensity with the plate reader.
3. Rotate the 96-well plate 180 degrees horizontally.
4. Measure the fluorescence intensity again.
5. Determine the auto-fluorescence of PBS by calculating the arithmetic mean of fluorescence intensity of PBS added in triplicate and use this value as the background fluorescence.
6. Subtract background fluorescence from each fluorescence intensity value of each well containing sodium fluorescein.
7. Take the arithmetic mean of the three technical replicates of sodium fluorescein of each concentration.
8. Draw the calibration curve.
-How to obtain the absolute unit of fluorescence intensity
1. Measure the fluorescence intensity with the plate reader.
2. Rotate the 96-well plate 180 degrees horizontally and measure the fluorescence intensity again.
3. Calculate the arithmetic mean of these two results.
4. Determine the auto-florescence of PBS by calculating the arithmetic mean of fluorescence intensity of PBS added in triplicate and use this value as the background fluorescence.
5. Subtract the background fluorescence from each well containing the samples.
6. Divide them by the value of OD590 of each sample.
7. Calculate the ng / mL fluorescence per OD590 unit by the formula we obtained from drawing the calibration curve.
4.4.2. Flow cytometer
Cells were gated according to the side scatter (SSC) and the forward scatter (FCS) to exclude cell debris and impurities.
4.5. Individuals responsible for conducting Interlab study
Misa Minegishi : Measured the devices and processed the data.
Yuta Yamazaki : Measured the devices and processed the data.
Hiraku Tokuma : Created the devices.
Riku Shinohara: Created the devices.
5. Reference