Description

This track is produced as part of the ENCODE Project. This track displays maps of histone modifications genome-wide in different cell lines, using ChIP-seq high-throughput sequencing.

Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here.

For each cell type, this track contains the following views:

HotSpots

ChIP-seq affinity zones identified using the HotSpot algorithm.

Peaks

ChIP-seq affinity sites identified as signal peaks within FDR 0.5% hypersensitive zones.

Raw Signal

Density graph (wiggle) of signal enrichment based on aligned read density.

Methods

Cells were grown according to the approved ENCODE cell culture protocols. Cells were crosslinked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibody at 4 degrees C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross linking in immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligated to Illumina adapters and made in to Solexa library for sequencing.

The sequencing reads uniquely mapping to the hg18 reference human genome were then scored using a scan statistic based on the binomial distribution. Regions of significant tag enrichment (significance being gauged using an FDR procedure based on randomly generated data) were then resolved into 150 bp peaks called on a continuous, sliding window tag density representation of the data (Sabo et al., 2004).

Verification

Data were verified by sequencing biological replicates displaying correlation coefficient >0.9.

Credits

These data were generated by the UW ENCODE group.

Contact: Richard Sandstrom

References

Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO, McArthur M, Stamatoyannopoulos JA. Discovery of functional noncoding elements by digital analysis of chromatin structure. PNAS. 2004;101:16837-16842.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here.