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Obtaining Survival Fractions using a Standard Spectrophotometer:

This tutorial describes how to obtain survival fractions using the YODA software with standard spectrophotometer /incubator / shaker combo.

Since YODA uses separate csv files for each point in the survival curve, csv files containing OD measurements will need to be split up. This example demonstrates how to obtain survival curves over increasing concentrations of a drug with a standard spectrophotometer.

1. Prepare a spectrophotometer plate with fresh media and inoculate treated cells into the plate (For a specific protocol for how we prepare a Bioscreen C plate with aging yeast cultures, see “Walkthrough”). Reserve a media only well to obtain the OD background due to media.
2. Measure the optical density (OD) for each well on the plate and record the OD values for each well and the time the reading was taken.
3. Incubate your spectrophotometer plate, while shaking, at the desired temperature until the next measurement interval.
4. Repeat step 2 until a complete growth curve for each well can be obtained.

See treatment_ods.csv for example file.

Since YODA calculates survival fractions across files, we need to split the 3 chemically treated cells (0mm, 30mm, and 60mm) into separate files. To do this:

1. Create a file “0mm.csv”
2. Copy from “treatment_ods.csv” the first column (time), the column corresponding to the 0mm control treatment, and the media only column (BLANK) into the “0mm.csv” file.
3. Save the file as a comma-separated value file (csv) without text-delimiters
4. Repeat steps 1-3 for each treatment

After completing steps 1-4 above, you will be left with 3 files, one for each treatment: “0mm.csv”, “30mm.csv”, and “60mm.csv”. These are the files you can input into YODA to calculate survival fractions for the various treatments.

See treatment.zip to see how the files should look going into YODA.

Under the “Upload” page, create a new experiment named “treatment”. The wells are assigned names using the well info format described in the “ Upload Help” section. See "naming.tsv" in treatment.zip for the well info input for this chemical treatment example (paste the contents into the “well info” input in the upload form). Add each of the 3 treatment files under "Runs" and make sure the day values of the runs match the order of the chemical treatments (day 1 => 0mm.csv, day 2 => 30mm.csv, day 3 => 60mm.csv). Note that the run with the earliest "day" value will be used as the reference curve for calculating relative time-shifts (and therefore survival fractions) for each file.

Figure 1.Upload the individual csv files for each treatment

Click the “upload” button to upload your experiment.

To analyze your data, go to the “Export” page and select the “treatment” experiment. Change “analyze” to “survivals” to output survival fractions and click “Export”. The survival fractions will be given for the strain for each of the different treatment files (see treatment_output.csv).

You can modify the steps above to obtain relative survival fractions for any number of treatments (they do not necessarily have to be in any particular order, except that the relative survival is always calculated using the time shift relative to the lowest "day" value).