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DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington   (ENC DNase/FAIRE)

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 All Treatment None  4-OHTAM 20 nM 72 hr  DIFF
4 d 		 diffProtA 2 d  diffProtA 5 d  diffProtA 9 d  diffProtA 14 d  Estradiol 100 nM
1 hr 		 Estradiol Control
0 hr 		TreatmentAll 
Cell Line Cell Line
GM12878 (Tier 1)   GM12878 (Tier 1)
H1-hESC (Tier 1)   H1-hESC (Tier 1)
K562 (Tier 1)   K562 (Tier 1)
A549 (Tier 2)   A549 (Tier 2)
B cells CD20+ RO01778 (Tier 2)   B cells CD20+ RO01778 (Tier 2)
HeLa-S3 (Tier 2)   HeLa-S3 (Tier 2)
HepG2 (Tier 2)   HepG2 (Tier 2)
HUVEC (Tier 2)   HUVEC (Tier 2)
LHCN-M2 (Tier 2)   LHCN-M2 (Tier 2)
MCF-7 (Tier 2)   MCF-7 (Tier 2)
Monocytes CD14+ RO01746 (Tier 2)   Monocytes CD14+ RO01746 (Tier 2)
AG04449   AG04449
AG04450   AG04450
AG09309   AG09309
AG09319   AG09319
AG10803   AG10803
AoAF   AoAF
BE2 C   BE2 C
BJ   BJ
Bone Marrow HS5   Bone Marrow HS5
Bone Marrow HS27a   Bone Marrow HS27a
Bone Marrow MSC   Bone Marrow MSC
Caco-2   Caco-2
CD4+ Naive Wb11970640   CD4+ Naive Wb11970640
CD4+ Naive Wb78495824   CD4+ Naive Wb78495824
CD34+ Mobilized   CD34+ Mobilized
CMK   CMK
GM04503   GM04503
GM04504   GM04504
GM06990   GM06990
GM12864   GM12864
GM12865   GM12865
H7-hESC   H7-hESC
HA-h   HA-h
HA-sp   HA-sp
HAc   HAc
HAEpiC   HAEpiC
HBMEC   HBMEC
HBVP   HBVP
HBVSMC   HBVSMC
HCF   HCF
HCFaa   HCFaa
HCM   HCM
HConF   HConF
HCPEpiC   HCPEpiC
HCT-116   HCT-116
HEEpiC   HEEpiC
HFF   HFF
HFF-Myc   HFF-Myc
HGF   HGF
HIPEpiC   HIPEpiC
HL-60   HL-60
HMEC   HMEC
HMF   HMF
HMVEC-dAd   HMVEC-dAd
HMVEC-dBl-Ad   HMVEC-dBl-Ad
HMVEC-dBl-Neo   HMVEC-dBl-Neo
HMVEC-dLy-Ad   HMVEC-dLy-Ad
HMVEC-dLy-Neo   HMVEC-dLy-Neo
HMVEC-dNeo   HMVEC-dNeo
HMVEC-LBl   HMVEC-LBl
HMVEC-LLy   HMVEC-LLy
HNPCEpiC   HNPCEpiC
HPAEC   HPAEC
HPAF   HPAF
HPdLF   HPdLF
HPF   HPF
HRCEpiC   HRCEpiC
HRE   HRE
HRGEC   HRGEC
HRPEpiC   HRPEpiC
HSMM   HSMM
HSMMtube   HSMMtube
HVMF   HVMF
Jurkat   Jurkat
LNCaP   LNCaP
M059J   M059J
NB4   NB4
NH-A   NH-A
NHBE RA   NHBE RA
NHDF-Ad   NHDF-Ad
NHDF-neo   NHDF-neo
NHEK   NHEK
NHLF   NHLF
NT2-D1   NT2-D1
PANC-1   PANC-1
PrEC   PrEC
RPMI-7951   RPMI-7951
RPTEC   RPTEC
SAEC   SAEC
SK-N-MC   SK-N-MC
SK-N-SH RA   SK-N-SH RA
SkMC   SkMC
T-47D   T-47D
Th1   Th1
Th1 Wb33676984   Th1 Wb33676984
Th1 Wb54553204   Th1 Wb54553204
Th2   Th2
Th2 Wb33676984   Th2 Wb33676984
Th2 Wb54553204   Th2 Wb54553204
Th17   Th17
Treg Wb78495824   Treg Wb78495824
Treg Wb83319432   Treg Wb83319432
WERI-Rb-1   WERI-Rb-1
WI-38   WI-38
Cell Line Cell Line
 All Treatment None  4-OHTAM 20 nM 72 hr  DIFF
4 d 		 diffProtA 2 d  diffProtA 5 d  diffProtA 9 d  diffProtA 14 d  Estradiol 100 nM
1 hr 		 Estradiol Control
0 hr 		TreatmentAll 
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  Cell Line↓1 Replicate↓2 views↓3   Track Name↓4    Restricted Until↓5
 
dense
 GM12878  1  HotSpots  GM12878 DNaseI HS HotSpots Rep 1 from ENCODE/UW    schema   2010-04-01 
 
dense
 GM12878  1  Peaks  GM12878 DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2010-04-01 
 
dense
 GM12878  1  Raw Signal  GM12878 DNaseI HS Raw Signal Rep 1 from ENCODE/UW    schema   2010-04-01 
 
dense
 GM12878  2  HotSpots  GM12878 DNaseI HS HotSpots Rep 2 from ENCODE/UW    schema   2010-04-01 
 
dense
 GM12878  2  Peaks  GM12878 DNaseI HS Peaks Rep 2 from ENCODE/UW    schema   2010-04-01 
 
dense
 GM12878  2  Raw Signal  GM12878 DNaseI HS Raw Signal Rep 2 from ENCODE/UW    schema   2010-04-01 
 
dense
 H1-hESC  1  HotSpots  H1-hESC DNaseI HS HotSpots Rep 1 from ENCODE/UW    schema   2010-06-18 
 
dense
 H1-hESC  1  Peaks  H1-hESC DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2010-06-18 
 
dense
 H1-hESC  1  Raw Signal  H1-hESC DNaseI HS Raw Signal Rep 1 from ENCODE/UW    schema   2010-06-18 
 
dense
 K562  1  HotSpots  K562 DNaseI HS HotSpots Rep 1 from ENCODE/UW    schema   2009-09-09 
 
dense
 K562  1  Peaks  K562 DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2009-09-09 
 
dense
 K562  1  Raw Signal  K562 DNaseI HS Raw Signal Rep 1 from ENCODE/UW    schema   2009-09-09 
 
dense
 K562  2  HotSpots  K562 DNaseI HS HotSpots Rep 2 from ENCODE/UW    schema   2009-09-09 
 
dense
 K562  2  Peaks  K562 DNaseI HS Peaks Rep 2 from ENCODE/UW    schema   2010-04-01 
 
dense
 K562  2  Raw Signal  K562 DNaseI HS Raw Signal Rep 2 from ENCODE/UW    schema   2009-09-09 
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Data version: ENCODE July 2012 Freeze

Description

This track was produced as part of the ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology (see below) and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promoters, locus control regions and novel elements. For each experiment (cell type), this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Raw Signal) and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks).

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
DNaseI sensitive zones identified using the HotSpot algorithm.
Peaks
DNaseI hypersensitive sites (DHSs) identified as signal peaks within FDR 1.0% hypersensitive zones.
Raw Signal
The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome).

DNaseI sensitivity is shown as the absolute density of in vivo cleavage sites across the genome mapped using the Digital DNaseI methodology (see below).

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. Digital DNaseI was performed by DNaseI digestion of intact nuclei, isolation of DNaseI 'double-hit' fragments as described in Sabo et al. (2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Illumina Geneome Analyzer II platform (36 bp reads). Uniquely mapping high-quality reads were mapped to the genome. DNaseI sensitivity is directly reflected in 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). DNaseI sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). False discovery rate thresholds of 1.0% (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm.

Verification

Data were verified by sequencing biological replicates displaying a correlation coefficient > 0.9. Results were extensively validated by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting methods.

Release Notes

This is release 6 (July 2012) of this track. It includes 11 new experiments across 12 new cell lines: bone marrow HS27a, bone marrow HS5, bone marrow MSC, CD4+ Naive Wb11970640, CD4+ Naive Wb78495824, Th17, Th1 Wb33676984, Th1 Wb54553204, Th2 Wb33676984, Th2 Wb54553204, Treg Wb78495824, Treg Wb83319432. This release also removes previously release K562 zinc-finger experiments. There are questions concerning the data due to a merging issue.

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.

Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods. 2006 Jul;3(7):511-8.

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.