Sunday, August 10, 2008

Deonier Ch 2 Codon Bias - Expression Data

Next, we want some expression data for E. coli genes. There are lots of sources for this, but I went to GEO, where I found the page shown in the screenshot. The study is described here.

It seemed like a good set because of the growth protocol: "wild type" cells pre-grown in rich medium, starved in salts, and then diluted in rich medium and grown for 90 minutes. Here is the description:

The cells are AB1157, which are quite a long way from their ancestral purity, but we'll ignore that:

The data are available in several formats including "Series Matrix" which is basically text

It's a simple matter to process this to a format with recognizable gene names, and values for the measured expression levels.