Two different 25-mer Affymetrix GeneChip oligonucleotide microarrays were used for the ChIP-chip analysis. One was a custom array, which densely tiled 20 kb upstream and 20 kb downstream of selected genes. The other was the Affymetrix mouse promoter array 1.0R . Hybridization and scanning of the custom tiling array was carried out using standard protocols and reagents from Affymetrix.

• IRF1 and NF-kB p50 ChIP-chip on custom Arrays (Unstimulated, and after LPS stimulation at 60min, 120min, 240min).
• PU1: 9 custom arrays (2 LPS time points + Unstimulated) + 3 promoter arrays (LPS 240 min)
• PolII: Unstim, and LPS 60, 120, 240, 360 min in triplicate on Affymetrix Promoter Arrays.

Further descriptions of the experiments and details of the processing are available. The table below can be sorted by experiment name, antibody used, time point, platform and stimulus used. For each experiment we provide:

• Tar achives contain all files for individual replicates (including CEL, BAR and BED files);
• BAR files for all replicates containing the MATscore for each probe (for use with the Affymetrix Integrated Genome Browser);
• BED files for all replicates containing the chromosome coordinates of all of the ChIP regions with MATscore; and
• TSV files for hits based on testing for consistency in 3 (higher_confidence) and 2 (lower_confidence) replicates.