The extracted DNA from #21 will be sequenced. The preparation for this is described here and previously performed by Leila here. However, eventual sequencing will be done by a company which may introduce different requirements. Enzo is in contact with them. Sending samples for sequencing will occur together with Enzo, sometime after the shutdown of the building (so in august). Results will then be in no sooner than september, probably october.
As the steps of this preparation have quite some waiting time these will have to be planned in advance
The preparation exists of:
Digestion (16 hours waiting time)
circularization of the DNA (6 hours waiting time + an overnight precipitation
PCR
To do:
[] Check with Enzo for any changes based on wishes of the sequencing company
So far it remains unclear. The company may do the PCR (for amplification). However we have to do the PCR +gel ourselves anyway to check if things went ok.
[] Check with Leila for any changes of protocol based on previous experience
[] Check if all materials are available
[] Fill in experimental template below
Hypothesis (We believe that...)
We believe that we can use benoit's protocol to prepare our extracted DNA for sequencing
Test (To verify that we will...)
To verify that we will perform the proctol on our DNA
False Test (To falsify that we should test...)
Metric (And measure...)
The lengths of digested genomic DNA with a gel, as well as the lengths of the PCR product
Criteria (We are right if...)
The observed digestion pattern and PCR product in the gels corresponds to the expected patterns shown in the protocol. For the PCR product, this should be one clear band indicating untransposed miniDs and a smear surrounding it. For the digestion it depends on which enzyme we use, but the DNA should be a smear and very short (~100 bp region).
Observation (We observed...)
We observed that the digestion pattern is as expected. The DNA is a smear, very short and very vague bands are visible in a similar manner to Leila's previous observation.
Learnings and insights (From that we learned that...)
The extracted DNA from #21 will be sequenced. The preparation for this is described here and previously performed by Leila here. However, eventual sequencing will be done by a company which may introduce different requirements. Enzo is in contact with them. Sending samples for sequencing will occur together with Enzo, sometime after the shutdown of the building (so in august). Results will then be in no sooner than september, probably october.
As the steps of this preparation have quite some waiting time these will have to be planned in advance The preparation exists of:
To do: [] Check with Enzo for any changes based on wishes of the sequencing company
Hypothesis (We believe that...) We believe that we can use benoit's protocol to prepare our extracted DNA for sequencing
Test (To verify that we will...) To verify that we will perform the proctol on our DNA
False Test (To falsify that we should test...)
Metric (And measure...) The lengths of digested genomic DNA with a gel, as well as the lengths of the PCR product
Criteria (We are right if...) The observed digestion pattern and PCR product in the gels corresponds to the expected patterns shown in the protocol. For the PCR product, this should be one clear band indicating untransposed miniDs and a smear surrounding it. For the digestion it depends on which enzyme we use, but the DNA should be a smear and very short (~100 bp region).
Observation (We observed...) We observed that the digestion pattern is as expected. The DNA is a smear, very short and very vague bands are visible in a similar manner to Leila's previous observation.
Learnings and insights (From that we learned that...)
Decisions and actions (Therefore we will...)