This track displays smoothed (sliding-window mean) scores for regions bound by Sp1 and Sp3 in the following three cell lines, assayed by ChIP and microarray hybridization:
Cell Line Classification Isolated From HCT 116 colorectal carcinoma colon Jurkat, Clone E6-1 acute T cell leukemia T lymphocyte K-562 chronic myelogenous leukemia (CML) bone marrow
This annotation follows the display conventions for composite tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.
Chromatin IP was performed as described in Trinklein et al. (2004). Amplified and labeled ChIP DNA was hybridized to oligo tiling arrays produced by NimbleGen along with a total genomic reference sample. The data for each array were median subtracted (log 2 ratios) and normalized (divided by the standard deviation).
The transformed mean ratios of ChIP DNA:Total DNA for all probes were then smoothed by calculating a sliding-window mean. Windows of six neighboring probes (sliding two probes at a time) were used; within each window, the highest and lowest value were dropped, and the remaining 4 values were averaged. To increase the contrast between high and low values for visual display, the average was converted to a score by the formula:
score = 8^(average) * 10. These scores are for visualization purposes; for all analyses, the raw ratios, which are available in the Stanf ChIP track, should be used.
Three biological replicates and two technical replicates were performed. The Myers lab is currently testing the specificity and sensitivity using real-time PCR.
These data were generated in the Richard M. Myers lab at Stanford University (now at HudsonAlpha Institute for Biotechnology).