β-galactosidase assay¶
The following layout was used to measure the expression of β-galactosidase in
different conditions. Particularly noteworthy are the fit_start_min and
fit_stop_min parameters. In this assay, the concentration of the enzyme is
deduced from a linear fit of absorbance over time (measured using a plate
reader). However, the reaction becomes non-linear as the substrate is
exhausted, which happens at different times for different conditions (i.e.
depending on how much enzyme is expressed). The fit_start_min and
fit_stop_min parameters specify which data points are in the linear regime.
The default is to use the data points between 5–30 min, but several wells use
different cutoffs to better fit the data. This is an good example of how the
fine-grained control provided by wellmap can be used to facilitate
analysis.
[expt]
spacer = 'lz'
ligand = 'theophylline'
fit_start_min = 5
fit_stop_min = 30
[row.A]
growth_time_h = 6
[row.B]
growth_time_h = 8
[row.C]
growth_time_h = 10
[row.D]
growth_time_h = 16
[col.3]
sgrna = 'on'
ligand_mM = 0
[col.4]
sgrna = 'on'
ligand_mM = 30
[col.5]
sgrna = 'off'
ligand_mM = 0
[col.6]
sgrna = 'off'
ligand_mM = 30
[well.B5]
fit_start_min = 0
fit_stop_min = 15
[well.C5]
fit_start_min = 5
fit_stop_min = 15
[well.D5]
fit_start_min = 0
fit_stop_min = 15
[well.D6]
fit_start_min = 0
fit_stop_min = 15
