RNA expression analysis using a 30 base pair resolution Escherichia coli genome array
Douglas W. Selinger, Kevin J. Cheung, Rui Mei, Eric M. Johansson, Craig S. Richmond, Frederick R. Blattner, David J. Lockhart, and George M. Church
Nature Biotechnology, Vol. 18: 1262-68, December 2000.
This page contains supplemental information for the paper by Selinger et al in Nature Biotechnology, December 2000. The data files are in tab-delimited form suitable for loading into a spreadsheet. To download a file, right click on the file name and select "Save Link As" (Netscape) or "Save Target As" (Internet Explorer) on the menu that appears.
The following links are for GAPS© and other resources related to high resolution analysis:
- GAPS© (Genome Array Processing Software)
- oligo sequences for the E. coli array
- high resolution data files generated by GAPS©
The following are guides to the files found on this site:
The following are ORF summary files, which describe the changes in relative RNA abundances:
The following are raw data files generated in our experiments. "CEL" files (7 MB) give intensities of all chip features, "DAT" files (44 MB) are raw image files. GAPS© uses "CEL" files as input. "CEL" files are generated by Genechip© from "DAT" files. NOTE: "DAT" files cannot be opened in your browser. Right-click on them and save them directly to your hard drive (see instructions at top of page).
These files are provided to allow others to analyze our raw data files using GeneChip©, GAPS©, or software of their own creation. We hope that it becomes common practice to provide the raw data from expression profiling experiments to allow innovative analyses from all sectors of the scientific community. In this spirit, we believe Affymetrix has done a service to the community by making the .CEL files "open source".
Note that "sense" chips are designed to hybridize to mRNA (Affymetrix Part No. 900284) and "antisense" chips are designed to hybridize with the reverse complement of mRNA (i.e., cDNA) (Not currently available commercially).
Please send questions and comments to Doug Selinger.