Growth Rate

This page outlines the experimental method and the subsequent processing for the cell line growth rate data derived from the GDSC cell line drug sensitivity screens.


Dataset Origin Data Type
GDSC Cell Line Growth Rates Sanger csv

Experimental Method

Cell model growth rates are calculated over the course of the GDSC drug sensitivity screens (cancerrxgene.org). These take place in 1536 well and 384 well plates where the duration of drug treatment is 72 hours. Cell viability measures are generated from independent assay plates at the beginning (day-1) and the end of drug treatment (day-4) using Cell Titer Glo 2.0 (Promega). Viability measurements for the negative control wells (DMSO treated) on the day-4 plates are compared to control wells (no treatment) on a day-1 plate matched by cell line, seeding density, plate type and plate date.

Due to the high-throughput nature of the GDSC drug screens the exact time delay between the two measurements may vary: in 15180 matched plates the mean time between the day-1 and day-4 measurement was 72.09 hours, the median was 72.10 hours, and the standard deviation 3.81 hours.

Replicate measurements have been made for most cell lines - median of 14 replicates, with 983 lines having 3 or more replicates. In many cases these replicates will have been measured over several years of experiments.

Processed Data

The GDSC Growth Estimate is reported as: day-4 to day-1 ratio +/- std_dev (num_replicates).

day-4 to day-1 ratio

The ratio of average fluorescence intensity of negative control wells taken at day-1 (time of dosing) and day-4 (end of assay, 72 hours after dosing). Negative control measurements are adjusted to background fluoresence as measured by blank wells containing media but no cells. The reported value is an average of available replicates.


The ratio of average fluorescence intensity of negative control wells taken at day-1 (time of dosing) and day-4 (end of assay, 72 hours after dosing). Negative control measurements are background corrected using the mean intensity of blank wells (media only, no cells) from the same assay plate. The reported value is an average of available replicates.

num_replicates

The number of replicate measurements used to calculate the day-4 to day-1 ratio.

std_dev

The standard deviation of the day-4 to day-1 ratio.

doubling time (hours)

The doubling time for the cell population calculated as: 72 hours / log2(day-4 day-1 ratio)