ENC TF Binding UW CTCF Binding Track Settings
 
CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington

Track collection: ENCODE Transcription Factor Binding

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  Replicate: 1 2 3
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Cell Line
GM12878 (Tier 1) 
K562 (Tier 1) 
A549 (Tier 2) 
B cells CD20+ RO01778 (Tier 2) 
B cells CD20+ RO01794 (Tier 2) 
HeLa-S3 (Tier 2) 
HepG2 (Tier 2) 
HUVEC (Tier 2) 
MCF-7 (Tier 2) 
Monocytes CD14+ RO01746 (Tier 2) 
AG04449 
AG04450 
AG09309 
AG09319 
AG10803 
AoAF 
BE2 C 
BJ 
Caco-2 
GM06990 
GM12801 
GM12864 
GM12865 
GM12872 
GM12873 
GM12874 
GM12875 
H7-hESC 
HAc 
HA-sp 
HBMEC 
HCF 
HCFaa 
HCM 
HCPEpiC 
HCT-116 
HEEpiC 
HEK293 
HFF 
HFF-Myc 
HL-60 
HMEC 
HMF 
HPAF 
HPF 
HRE 
HRPEpiC 
HVMF 
Jurkat 
LNCaP 
NB4 
NHDF-neo 
NHEK 
NHLF 
PANC-1 
RPTEC 
SAEC 
SkMC 
SK-N-MC 
SK-N-SH RA 
WERI-Rb-1 
WI-38 
Cell Line
 All Factor CTCF  Input 
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 GM12878  CTCF  1  Hotspots  GM12878 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW    Data format   2010-03-29 
 
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 GM12878  CTCF  2  Hotspots  GM12878 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW    Data format   2010-06-20 
 
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 GM12878  CTCF  1  Peaks  GM12878 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW    Data format   2010-03-29 
 
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 GM12878  CTCF  2  Peaks  GM12878 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW    Data format   2010-03-29 
 
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 GM12878  CTCF  1  Raw Signal  GM12878 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW    Data format   2010-03-29 
 
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 GM12878  CTCF  2  Raw Signal  GM12878 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW    Data format   2010-06-20 
 
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 GM12878  Input  1  Raw Signal  GM12878 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW    Data format   2011-03-09 
 
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 K562  CTCF  1  Hotspots  K562 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW    Data format   2010-03-29 
 
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 K562  CTCF  2  Hotspots  K562 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW    Data format   2010-06-20 
 
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 K562  CTCF  1  Peaks  K562 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW    Data format   2010-03-29 
 
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 K562  CTCF  2  Peaks  K562 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW    Data format   2010-03-29 
 
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 K562  CTCF  1  Raw Signal  K562 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW    Data format   2010-03-29 
 
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 K562  CTCF  2  Raw Signal  K562 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW    Data format   2010-06-20 
 
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 K562  Input  1  Raw Signal  K562 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW    Data format   2011-03-09 
     Restriction Policy
Assembly: Human Feb. 2009 (GRCh37/hg19)

Description

This track was produced as part of the ENCODE Project. This track displays maps of genome-wide binding of the CTCF transcription factor 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 affinity zones (FDR 1.0%).
Raw Signal
The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome).

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

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 antibodies at 4 °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. A quantity of 20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and a Solexa library was made for sequencing.

ChIP-seq affinity was directly measured through raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004); 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. ChIP-seq affinities (Peaks) were identified as signal peaks within affinity zones (FDR 1.0%) using a peak-finding algorithm.

All tracks have a False Discovery Rate of 1% (FDR 1.0%).

Verification

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

Release Notes

Release 3 (February 2012) contains 3 new experiments.

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 et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42.

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.