Description

ChIP analysis was performed using antibodies to E2F1 and C-Myc in HeLa cells. E2F1 and C-Myc protein are transcription factors related to growth. E2F1 is important in controlling cell division, and C-Myc is associated with cell proliferation and neoplastic disease. 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 conditions.

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Methods

Ratio intensity values (antibody 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.

Verification

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.

Credits

These data were contributed by Mike Singer, Kyle Munn, Nan Jiang, Todd Richmond and Roland Green of NimbleGen Systems, Inc., and Matt Oberley, David Inman, Mark Bieda, Shally Xu and Peggy Farnham of Farnham Lab.