ENCODE region-wide location analyses of TAF1 binding and RNA polymerase II (pre-initiation complex form) binding were conducted using chromatin extracted from IMR90 (lung fibroblast), HCT116 (colon epithelial carcinoma), HeLa (cervix epithelial adenocarcinoma), and THP1 (blood monocyte leukemia) cells.
Chromatin from each of the four cell lines was separately cross-linked, precipitated with antibody to one of the two enzymes, sheared, amplified and hybridized to a DNA array. The Ren Lab at UC San Diego produced a PCR tiling array composed of 24,537 non-repetitive sequences within the 44 ENCODE regions.
For each marker, there are three biological replicates. Each experiment is normalized using their median values; the P-value and R-value are calculated using the modified single array error model (Li, Z. et al., 2003). The P-value and R-value are then derived from the weighted average results of the replicates.
The scale is 0-16, corresponding to negative log base 10.
There are three biological replicates for each of the eight experiments.
The array platform, the raw and normalized data for each experiment, and the image files have all been deposited at the NCBI GEO Microarray Database.
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