Randomized fragment

I am back from vacation and what a better way to shake my mind than a blog post! Before my vacation break, I was trying to make a double stranded 200 bp fragment with a randomized region by using two different long oligos. One 135 bp with a 70 randomized bases and a 30 bases overlapping region with the… More Randomized fragment

Oligos

Lately I have been working on generating a 200 bp fragment  that will contain a 69 bp randomized region. I will do this by using two large oligos with a 30bp overlapping region. As shown in the figure below, the right oligo has a illumina sequencing primer site, extra bases and the overlapping region. On… More Oligos

Peak Finder

As discussed extensively in previous posts, our analysis of DNA uptake data in Haemophilus influenzae is going very well. So far it seems that most of the variation in DNA uptake across the genome are explained by the proximity to an uptake signal sequence (USS).  We have scored the genome using two distinct uptake motif models. The first… More Peak Finder

Data analysis plan

Finally, I got the sequencing data from a project I had been working on. This project is trying to determine the factors explaining why some regions of Haemophilus influenzae genome are taken up more than others by competent cells in DNA uptake experiments. To answer this question, I did a series of uptake experiments using… More Data analysis plan

Exposure vs Dose

My supervisor asked to calculate my radioactive exposure, after working with P32, for our annual radioactivity report. My first thought was that don’t remember very well how to do that calculation, so I went back to the radioactivity manual I got during my training. I looked for a formula to calculate exposure and I see that… More Exposure vs Dose

P-32 calculations

  The next step in my calculations is to determine how many nanograms of perfectly labelled sheared DNA would I have to load in the gel to see the size distribution with the phosphoimager. To calculate this, first I need to know how many dpm in a band I need to see it using a phosphoimager.  … More P-32 calculations

Math

Hi blog, long time no see…. I am about to receive P-32 ATP for DNA uptake experiments and I need to think in some calculations that will be necessary to be able to determine the efficiency of the labeling reaction using sheared genomic DNA as input DNA. In order to determine the efficiency of the… More Math