Experimental Data - ChIP-Seq
Immunoprecipitated chromatin was analyzed using the Illumina Genome Analyzer, a massively parallel sequencing system. Cells were grown, treated, and harvested in the same manner as those for ChIP-on-chip analysis. The purified DNA was processed using Illumina's protocols and reagents. Please see our Protocols - ChIP-Seq page.

ChIP-Seq Data output is a collection of peaks indicating enrichment of specific sequences in the chromatin immunoprecipitation. For each ChIP-seq experiment, two processed data files are available describing the locations of the binding regions, a BAR file and a BED file. The BAR file is a binary file format (defined by Affymetrix) that provides the count of overlapping extended fragments (in tags per million) at survey points that fall within the binding region as detected by the peak-finding algorithm (see Data Analysis Methods in the Protocols section). The BED file is a tab-delimited text file that describes the chromosomal coordinates and maximum height (in tags per million) of each binding region (peak region). Both the BAR and BED files can be opened in the Affymetrix IGB genome browser, to display the binding data in the context of the annotated reference genome. In addition, the BED files can be uploaded to the Web-based UCSC genome browser and displayed or analyzed using a variety of tools available on that website. Finally, by renaming a BED file to have the ".txt" filename extension, the file can be opened as a spreadsheet in Microsoft Excel. The table below contains BAR and BED files for each experiment.

• BAR files can be loaded into the IGB genome browsing program from Affymetrix for viewing ChIP-Seq data in its chromosomal context.
• BED file is a text-based genome annotation file that can be opened in Excel or loaded into the UCSC Genome Browser.