LI ChIP Various Track Settings
 
Ludwig Institute/UCSD ChIP-chip: Pol2 8WG16, TAF1, H3ac, H3K4me2, H3K27me3 antibodies   (LI/UCSD ChIP)

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 LI Pol2 HeLa  Ludwig Institute ChIP-chip: Pol2 8WG16 ab, HeLa cells   schema 
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 LI Pol2 THP1  Ludwig Institute ChIP-chip: Pol2 8WG16 ab, THP1 cells   schema 
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 LI Pol2 IMR90  Ludwig Institute ChIP-chip: Pol2 8WG16 ab, IMR90 cells   schema 
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 LI Pol2 HCT116  Ludwig Institute ChIP-chip: Pol2 8WG16 ab, HCT116 cells   schema 
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 LI TAF1 HeLa  Ludwig Institute ChIP-chip: TAF1 ab, HeLa cells   schema 
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 LI TAF1 THP1  Ludwig Institute ChIP-chip: TAF1 ab, THP1 cells   schema 
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 LI TAF1 IMR90  Ludwig Institute ChIP-chip: TAF1 ab, IMR90 cells   schema 
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 LI TAF1 HCT116  Ludwig Institute ChIP-chip: TAF1 ab, HCT116 cells   schema 
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 LI H3ac IMR90  Ludwig Institute ChIP-chip: H3ac ab, IMR90 cells   schema 
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 LI H3K4me2 IMR90  Ludwig Institute ChIP-chip: H3K4me2 ab, IMR90 cells   schema 
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 LI SUZ12 HeLa  Ludwig Institute ChIP-chip: SUZ12 protein ab, HeLa cells   schema 
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 LI H3K27me3 HeLa  Ludwig Institute ChIP-chip: H3K27me3 ab, HeLa cells   schema 
    
Data version: ENCODE June 2005 Freeze
Data coordinates converted via liftOver from: July 2003 (NCBI34/hg16)

Description

ENCODE region-wide location analyses were conducted of binding to the initiation-complex form of RNA polymerase II (Pol2), TATA-associated factor (TAF1), acetylated histone H3 (H3ac), lysine-4-dimethylated H3 (H3K4me2), suppressor of zeste 12 protein homolog (SUZ12), and lysine-27-tri-methylated H3 (H3K27me3). The analyses used chromatin extracted from IMR90 (lung fibroblast), HCT116 (colon epithelial carcinoma), HeLa (cervix epithelial adenocarcinoma), and THP1 (blood monocyte leukemia) cells. The initiation-complex form of Pol2 is associated with the transcription start site, as is TAF1. Both H3ac and H3K4me2 are associated with transcriptionally-active "open" chromatin.

Display Conventions and Configuration

This annotation follows the display conventions for composite tracks. Data for each antibody/cell line pair is displayed in a separate subtrack. See the top of the track description page for a complete list of the subtracks available for this annotation. The subtracks 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 the 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.

Methods

Chromatin from each of the four cell lines was separately cross-linked, precipitated with antibody to one of the six proteins, sheared, amplified and hybridized to a PCR DNA tiling array produced at the Ren Lab at UC San Diego. The array was composed of 24,537 non-repetitive sequences within the 44 ENCODE regions.

For each marker, there were three biological replicates. Each experiment was normalized using the median values. The P-value and R-value were calculated using the modified single array error model (Li, Z. et al., 2003). The P-value and R-value were then derived from the weighted average results of the replicates.

The displayed values were scaled to 0 - 16, corresponding to negative log base 10 of the P-value.

Verification

Each of the experiments has three biological replicates. 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.

Credits

The data for this track were generated at the Ren Lab, Ludwig Institute for Cancer Research at UC San Diego.

References

Kim, T., Barrera, L.O., Qu, C., van Calcar, S., Trinklein, N., Cooper, S., Luna, R., Glass, C.K., Rosenfeld, M.G., Myers, R., Ren, B. Direct isolation and identification of promoters in the human genome. Genome Research 15,830-839 (2005).

Li, Z., Van Calcar, S., Qu, C., Cavenee, W.K., Zhang, M.Z., and Ren, B. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc. Natl. Acad. Sci. 100(14), 8164-8169 (2003).

Ren, B., Robert, F., Wyrick, J. W., Aparicio, O., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert , T. L., Wilson, C., Bell, S. P. and Young, R. A. Genome-wide location and function of DNA-associated proteins Science 290(5500), 2306-2309 (2000).