Supplementary information for:

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:

• directory contains data files and documents.
• Supplement Guide - Document that describes the data file fields, the .CEL files that are available, and provides some technical notes for the paper.

The following are ORF summary files, which describe the changes in relative RNA abundances:

• LPvsSP_2max_rpt.txt - Log phase versus stationary phase, including genomic DNA data. The full data file in the form loaded into ExpressDB.
• stat1_cDNA_revcomp_rpt.txt - Reverse complement analysis of first stationary phase chip using a cDNA labeling protocol (4-8max).
• log_RNA_revcomp_rpt.txt - Reverse complement analysis of a log phase sample using the Affymetrix RNA labeling protocol (4-8max).

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).

• log1.CEL, log1.DAT - Antisense chip of log phase cells, labeled cDNA sample (replicate 1)
• log2.CEL, log2.DAT - Antisense chip of log phase cells, labeled cDNA sample (replicate 2)
• stat1.CEL, stat1.DAT - Antisense chip of stationary phase cells, labeled cDNA sample (replicate 1)
• stat2.CEL, stat2.DAT - Antisense chip of stationary phase cells, labeled cDNA sample (replicate 2)
• gDNA.CEL - Antisense chip of labeled genomic DNA
• stat1_cDNA_revcomp.CEL - Sense chip of stationary phase cells, labeled cDNA sample (from replicate 1). This is a reverse complement analysis in that it is probing the strand opposite of the one the chip was designed to target (discussed in the paper)
• log_RNA_revcomp.CEL - Antisense chip of directly labeled RNA, according to Affymetrix's protocol. This is a reverse complement analysis. The RNA sample was from a different LB culture than log1 and log2 above.
• Normalization Parameters - The background and scaling factor values used in the GAPS^© analyses of these files.

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.