Schema for UW Histone - ENCODE Histone Modifications by Univ. Washington ChIP-seq
  Database: hg18    Primary Table: wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf    Row Count: 136,573   Data last updated: 2009-09-21
Format description: Wiggle track values to display as y-values (first 6 fields are bed6)
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 164int(10) unsigned range Start position in chromosome
chromEnd 7444int(10) unsigned range End position in chromosome
name chr1.0varchar(255) values Name of item
span 20int(10) unsigned range each value spans this many bases
count 364int(10) unsigned range number of values in this block
offset 0int(10) unsigned range offset in File to fetch data
file /gbdb/hg18/wib/wgEncodeUwCh...varchar(255) values path name to data file, one byte per value
lowerLimit 1double range lowest data value in this block
dataRange 5double range lowerLimit + dataRange = upperLimit
validCount 48int(10) unsigned range number of valid data values in this block
sumData 144double range sum of the data points, for average and stddev calc
sumSquares 614double range sum of data points squared, for stddev calc

Sample Rows
 
binchromchromStartchromEndnamespancountoffsetfilelowerLimitdataRangevalidCountsumDatasumSquares
585chr11647444chr1.0203640/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib1548144614
585chr14490448364chr1.120173364/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib10353535
585chr18124496784chr1.220777537/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib121292153997
586chr1224064242784chr1.3209361314/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib11201301306116186
586chr1244724245384chr1.420332250/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib10171717
587chr1314544314724chr1.52092283/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib2091836
588chr1451884452064chr1.62092292/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib10999
73chr1511224530604chr1.7209692301/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib1477151216664
589chr1533644553364chr1.8209863270/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib110375102291072
589chr1554384571564chr1.9208594256/gbdb/hg18/wib/wgEncodeUwChIPSeqRawSignalRep2Gm12878Ctcf.wib150166105841854

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

UW Histone (wgEncodeUwChIPSeq) Track Description
 

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.