Author: Prof. Andresen

This morning, Lauren and I finished diluting our samples from the spinning yesterday and ran them in the spectrometer. After lunch, she analyzed the data while I started on a new calibration set. We still have enough of the previous set for a few more runs. The percent errors on the new set are very low so hopefully it will be as good as the previous set.

This morning I looked a the data from the last test run.  It came out really well, all the concentrations were consistent with each other, percent errors were low.  So we decided to do the real run aka same experiment just adding nucleosomes.  So Brian and I made up new samples and spent the afternoon spinning them.  We decided to keep the calibration set from last time, because there is enough for a few more runs and as you could see from the picture, very correlated!  Not enough time to run the spectrometer today, but we’ll do that tomorrow and see how everything went.

This morning I read an article about DNA condensation while Lauren analyzed the data from yesterday. After discussing her findings with Prof. Andresen, we started making samples to run an actual experiment with. After lunch we went to the cold room to spin these samples. We spun 8 times, collecting the sample after spin 7, spin 8, and after we flipped the filter.

This morning I went to the cold room in the science center to spin samples. This took me up until lunch. After lunch, I finished making these samples to be run in the spectrometer. I collected the spin through liquid from spins 7 and 8. I also collected what was left in the tubes after all the spins. We will see the results of the samples tomorrow.

This picture deserves a post of it’s own.  Except for that one point, this is the most beautiful correlation I have ever made with the spectrometer.

Fairly calm day.  Went over the data this morning.  The Spin 7 and Buffer samples came back consistent with each other.  However the left over samples were incredibly high, way too high.  I’m pretty sure it’s because I messed up that part, when I flipped the filter for the spin I accidentally put it in the same tube, not a new one.  Also I forgot to do a spin 8….incidentally Brian and I spent the afternoon making new samples and calibrations.  We ran the calibrations to make sure there were ok, but it looks like we’ll have to re-do them tomorrow morning, since the magnesium and phosphorus correlation weren’t very good.  And tomorrow we are going to go to the cold room again and do the experiment right this time.  (And also bring a sweater ^_^)

Friday was fairly uneventful.  This morning I ran the samples in the centrifuge in the cold room.  I was very cold, but managed to get it done before lunch.  Realized I should have run the spin one more time to get the spin 8 samples, so I only have the leftover sample, spin 7, and buffer to run in the spectrometer.  Ran the spectrometer in the afternoon.  Will start analyzing data Monday.

This morning I ran calibrations in the spectrometer to make sure they were good enough to run samples. The results were good. So in the afternoon, I helped Lauren prepare samples. Then we ran the spectrometer. We will look at the results on Monday.

So yesterday I ran three more trials on the spectrometer to measure Sodium.  After running about half the trials, I realized I put 1/10 the amount of cobalt I should have.  No worries, I just took out the internal standard in the analysis part!  Got back 2.81% error of the 0.6 ppm sample and 2.29% error on the 0.8 ppm sample.   That was after averaging all the data together.  Not too shabby!

ps, can’t get the formatting on that right….

So today we moved on to doing a trial run with out the nucleosomes.  Basically making up the samples to be spun and then run in the spectrometer and the calibration set.  I struggled all day with the calibrations and the pipets… But it’s all ready to be run tomorrow!

This morning Professor Andresen and I put the samples into the gel. Then we plugged it into a power source and let it run for a few hours. After lunch, we went to the science center. We put the gel into ethidium bromide. After we rinsed off the excess, we put it into another machine to see what the samples did. It turned out that our nucleosome supply is still mostly good.
When we got back I helped Lauren on her project by making her buffers.