ChIP analysis was performed using an antibody to E2F1 and HeLa cell chromatin. E2F1 is a transcription factor important in controlling cell division. Three independently crosslinked preparations of HeLa cells were used to provide three independent biological replicates. ChIP assays were performed (with minor modifications which can be provided upon request) using the protocol found at The Farnham Laboratory. Array hybridizations were performed using standard NimbleGen Systems Inc. conditions.
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Ratio intensity values (E2F1 vs. total) for each of three biological replicates were calculated and converted to log2. Each set of ratio values was then independently scaled by its Tukey bi-weight mean. The three replicates were then combined by taking the median scaled log2 ratio for each oligo.
Primers were chosen to correspond to 13 individual peaks. PCR reactions were performed for each of the 13 primer sets using amplicons derived from each of three biological samples (39 reactions). The PCR reactions confirmed that all of the 13 chosen peaks were bound by E2F1 in all three biological samples.
These data were contributed by Mike Singer, Kyle Munn, Nan Jiang, Todd Richmond and Roland Green of NimbleGenSystems, Inc., and Matt Oberley, David Inman, Mark Bieda, Shally Xu and Peggy Farnham of Farnham Lab.