Deadline: 15.12.2023 Friday 23:30 (11:30 P.M.

Bonus Assignment
Below is the agarose gel electrophoresis result of two fragments. The ladder used here is “1 kb
Plus DNA Ladder” by Thermo Fisher. There are two possible ways to determine the size of these
fragments. You can simply compare the bands to the ladder and roughly estimate the sizes.
Alternatively, you can plot the graph between the sizes of ladder fragments in logarithmic scale
and the distance travelled by these fragments. Since there is a linear relationship between the
two variables, you can then plot the trendline and obtain the formula. Finally, you can measure
the distance travelled by the two bands and obtain the size by using the formula. Note that the
formula will give you the size in log10; you need to antilog to get the actual length in base pairs.

For this assignment, please label the photo by indicating

the sizes of key fragments in the ladder. Estimate the sizes
of the two bands and state it verbally. Note that your
estimation cannot be exact at this point. Measure the
distance travelled by each fragment of ladder (you can
simply print out the figure and measure by a ruler) and
make a table as in the example. Plot the scatter graph and
add a trend line. Obtain the formula. Make sure you have
decent graphs; axes labelled, ranges adjusted, trendline
and formula added. Measure the distance travelled by the
two fragments and find their sizes by using the formula.
Show your calculations clearly.
Note that since you will use different measurement
methods and you will have different sizes of the figure,
each of you should obtain slightly different results. Do not
copy and paste from each other.
You can follow below screenshots for guidance. You can
use Excel to plot your graphs. However, you should upload
a word file at the end with the graph, figure, table,
calculations and your verbal explanations.
Deadline: 15.12.2023 Friday 23:30 (11:30 P.M.)

Select the distances and log(bp) columns; click on “Insert” and select scatter plot. This will plot a basic
graph. You need to make some adjustments to make the graph more presentable.

Axes have a wider range than our dataset.

You can adjust the minimum bound to see
your datapoints better. For example in this
case, for the x-axis, we don’t have any
datapoints smaller than 1.5; so I’ll set 1.5 as
my minimum bound. You need to do it for
both axes.

You need to add axis titles; on the

x-axis you should have the
distance travelled by the
fragments in cm; on the y-axis you
should have the sizes of
fragments in log(bp).

Finally, you need to

add a trendline; make
sure it is linear.
Deadline: 15.12.2023 Friday 23:30 (11:30 P.M.)

Click on the line; you will have

a tab opened.

In

this tab you can change some options for the trendline. You need to click on
“Display Equation on chart” to see the equation.

For example, for my graph I have “y = -0.3561x + 4.3082”. If I measure the

distance travelled by an unknown fragment, I can write that value in the
place of “x” and obtain the “y” which would be the size in log(bp). Taking the
antilog of that value, I could obtain the actual size of the fragment in base
pairs.