Tag Archives: PCR

Last lab guys!

We are approaching the end of a cycle… during this genomics laboratory you put your hands on genome sequencing and finishing, and of course you had a nice «primer» on Perl programming, perhaps with a boost in your primer design skills as an extra bonus.

It’s time to sum up, with a «self service» laboratory…

Due to the remarkable success of this year laboratory, that has been an experiment I wanted to try, we will repeat the 20 hours “Perl practical” next year. So stay tuned 🙂

See you this afternoon,


Refresh your Perl, the size you want.

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Calculate your oligonucleotide resuspension volume

As promised during today’s lecture, here you have your homework:

please calculate the amount  of water to be added to each of the primers in the list, in order to produce a working solution of 10 µM. You can produce a concentrated stock solution and then dilute the stock solution to a working solution of 10 µM, if it is needed.

Oligonucleotide datasheet containing all the information as provided by the supplier

Did you managed to find the right volume for each stock solution?

The Hamilton pipetter needs you to provide a coordinate and a volume separated by a tab for each of the primer. The information concerning each of the primers must be separated by a new line character, as shown in the example below

example of coordinate's file that you should pass to the Robot, to guide it (him?) doing the pipetting for you

Now try to translate the work that you performed to get this result into a list of actions (the algoritm).

For the most willing students, this is the moment for translating your algoritm into a Perl program and testing it at volume calculation for this short primer’s list.

Very soon you will find the solution on this blog. Stay tuned

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Lab Groups

In attachment to this post you will find the list of students divided in 7 groups. There are 5 groups of 4 students and 2 groups of 3 students. You can change group as long as you find a friend who agrees to perform the exchange and as long as the exchange fits these three simple roules:

  • groups number 1, 2, 3, 4 and 5 must be composed of 4 people
  • groups number 6 and 7 must be composed of 3 people
  • Annagiulia, Tea and Ilaria must not be moved from the assigned group
remember to bring you lab coat and a calculator with you
see you soon in the labs

groups list 

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wet lab

Time to test experimentally your work on the computer!

Your primers were successfully ordered and will be delivered soon. As anticipated during the introduction to the laboratory, the primers will be resuspended in ultrapure water (to a concentration of 100µM) and diluted to obtain a working solution (concentration 10µM) using an automated system that makes the pipetting for us, as long as we pass to it the correct instructions.

As you experimented during the first part of this laboratory experience, being able to translate your practice into a list of actions to be carried out, makes you able to tell a computer to do something for you. You can also instruct the computer to drive a machine to carry out the work for you 😉

So only for this time we will let you run you PCRs by you selves.. next time you’ll be able to ask a robot to assembly them for you! Maybe I’m just joking.. but not that much.. find it out yourselves following this link.

Next week we will start with some practice about PCR and we will also produce our useful data to close a few gaps of the genome. Following this link  (Wetlab protocol) you will find a copy of the laboratory protocol. Have a look at it. You will also find a copy on the lab bench, so no need to print it and bring it to the labs.

Instructions are really detailed even though many of you will have run a PCR before. Nevertheless there are a few advantages:

  • provide you with enough instructions to be as more autonomous as possible
  • use as much technical vocabulary as possible to help improve you english
  • induce you to a correct lab practice
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