ENC DNase/FAIRE Duke DNaseI HS Track Settings
 
Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)

Track collection: ENCODE Open Chromatin by DNaseI HS and FAIRE

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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+ RO01794 (Tier 2)   B cells CD20+ RO01794 (Tier 2)
HeLa-S3 (Tier 2)   HeLa-S3 (Tier 2)
HepG2 (Tier 2)   HepG2 (Tier 2)
HUVEC (Tier 2)   HUVEC (Tier 2)
IMR90 (Tier 2)   IMR90 (Tier 2)
MCF-7 (Tier 2)   MCF-7 (Tier 2)
Monocytes CD14+ (Tier 2)   Monocytes CD14+ (Tier 2)
SK-N-SH (Tier 2)   SK-N-SH (Tier 2)
8988T   8988T
Adult CD4+ Th0   Adult CD4+ Th0
Adult CD4+ Th1   Adult CD4+ Th1
AoSMC   AoSMC
Cerebellum OC   Cerebellum OC
Cerebrum frontal OC   Cerebrum frontal OC
Chorion   Chorion
CLL   CLL
Colo829   Colo829
ECC-1   ECC-1
Fibrobl   Fibrobl
Fibrobl GM03348   Fibrobl GM03348
FibroP AG08395   FibroP AG08395
FibroP AG08396   FibroP AG08396
FibroP AG20443   FibroP AG20443
Frontal cortex OC   Frontal cortex OC
GC B cell   GC B cell
Gliobla   Gliobla
GM10248   GM10248
GM10266   GM10266
GM12891   GM12891
GM12892   GM12892
GM13976   GM13976
GM13977   GM13977
GM18507   GM18507
GM19238   GM19238
GM19239   GM19239
GM19240   GM19240
GM20000   GM20000
H7-hESC   H7-hESC
H9ES   H9ES
Heart OC   Heart OC
HEK293T   HEK293T
Hepatocytes   Hepatocytes
HMEC   HMEC
HPDE6-E6E7   HPDE6-E6E7
HSMM   HSMM
HSMM emb   HSMM emb
HSMM FSHD   HSMM FSHD
HSMMtube   HSMMtube
HTR8svn   HTR8svn
Huh-7   Huh-7
Huh-7.5   Huh-7.5
iPS CWRU1   iPS CWRU1
iPS NIHi7   iPS NIHi7
iPS NIHi11   iPS NIHi11
Ishikawa   Ishikawa
LNCaP   LNCaP
Medullo   Medullo
Medullo D341   Medullo D341
Mel 2183   Mel 2183
Melano   Melano
Myometr   Myometr
Naive B cell   Naive B cell
NHEK   NHEK
Olfactory neurosphere   Olfactory neurosphere
Osteoblasts   Osteoblasts
PanIsletD   PanIsletD
PanIslets   PanIslets
pHTE   pHTE
ProgFib   ProgFib
Psoas muscle OC   Psoas muscle OC
RWPE1   RWPE1
Stellate   Stellate
T-47D   T-47D
Urothelia   Urothelia
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 GM12878      Peaks  GM12878 DNaseI HS Peaks from ENCODE/Duke    Data format   2009-12-20 
 
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 GM12878      Density Signal  GM12878 DNaseI HS Density Signal from ENCODE/Duke    Data format   2009-11-27 
 
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 GM12878      Overlap Signal  GM12878 DNaseI HS Overlap Signal from ENCODE/Duke    Data format   2009-11-27 
 
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 H1-hESC      Peaks  H1-hESC DNaseI HS Peaks from ENCODE/Duke    Data format   2010-06-30 
 
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 H1-hESC      Density Signal  H1-hESC DNaseI HS Density Signal from ENCODE/Duke    Data format   2010-06-30 
 
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 H1-hESC      Overlap Signal  H1-hESC DNaseI HS Overlap Signal from ENCODE/Duke    Data format   2010-06-30 
 
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 K562      Peaks  K562 DNaseI HS Peaks from ENCODE/Duke    Data format   2012-11-28 
 
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 K562      Density Signal  K562 DNaseI HS Density Signal from ENCODE/Duke    Data format   2012-11-28 
 
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 K562      Overlap Signal  K562 DNaseI HS Overlap Signal from ENCODE/Duke    Data format   2012-11-28 
     Restriction Policy
Source data version: ENCODE July 2012 Freeze
Assembly: Human Feb. 2009 (GRCh37/hg19)

Description

These tracks display DNaseI hypersensitivity (HS) evidence as part of the four Open Chromatin track sets. DNaseI is an enzyme that has long been used to map general chromatin accessibility and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions, and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome.

Together with FAIRE and ChIP-seq experiments, these tracks display the locations of active regulatory elements identified as open chromatin in multiple cell types from the Duke, UNC-Chapel Hill, UT-Austin, and EBI ENCODE group. Within this project, open chromatin was identified using two independent and complementary methods: these DNaseI HS assays and Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE), combined with chromatin immunoprecipitation (ChIP) for select regulatory factors. DNaseI HS and FAIRE provide assay cross-validation with commonly identified regions delineating the highest confidence areas of open chromatin. ChIP assays provide functional validation and preliminary annotation of a subset of open chromatin sites. Each method employed Illumina (formerly Solexa) sequencing by synthesis as the detection platform. The Tier 1 and Tier 2 cell types were additionally verified using high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen.

Other Open Chromatin track sets:

  • Data for the FAIRE experiments can be found in UNC FAIRE.
  • Data for the ChIP experiments can be found in UTA TFBS.
  • A synthesis of all the open chromatin assays for select cell lines can be previewed in Open Chrom Synth.

Display Conventions and Configuration

This track is a multi-view composite track that contains a single data type with multiple levels of annotation (views). For each view, there are multiple subtracks representing different cell types that display individually on the browser. Instructions for configuring multi-view tracks are here. Chromatin data displayed here represents a continuum of signal intensities. The Crawford lab recommends setting the "Data view scaling: auto-scale" option when viewing signal data in full mode to see the full dynamic range of the data. Note that in regions that do not have open chromatin sites, autoscale will rescale the data and inflate the background signal, making the regions appear noisy. Changing back to fixed scale will alleviate this issue. In general, for each experiment in each of the cell types, the Duke DNaseI HS tracks contain the following views:

Peaks
Regions of enriched signal in DNaseI HS experiments. Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle et al., 2008b). Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. The solid vertical line in the peak represents the point with the highest signal.

F-Seq Density Signal
Density graph (wiggle) of signal enrichment calculated using F-Seq for the combined set of sequences from all replicates. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). This method does not look at fixed-length windows, but rather weights contributions of nearby sequences in proportion to their distance from that base. It only considers sequences aligned 4 or less times in the genome and uses an alignability background model to try to correct for regions where sequences cannot be aligned. For each cell type (especially important for those with an abnormal karyotype), a model to try to correct for amplifications and deletions that is based on control input data was also used.

Base Overlap Signal
An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair.

Peaks and signals displayed in this track are the results of pooled replicates. The raw sequence and alignment files for each replicate are available for download.

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.

DNaseI hypersensitive sites were isolated using methods called DNase-seq or DNase-chip (Song and Crawford, 2010; Boyle et al., 2008a; Crawford et al., 2006). Briefly, cells were lysed with NP40, and intact nuclei were digested with optimal levels of DNaseI enzyme. DNaseI-digested ends were captured from three different DNase concentrations, and material was sequenced using Illumina (Solexa) sequencing. DNase-seq data for Tier 1 and Tier 2 cell lines were verified by comparing multiple independent growths (replicates) and determining the reproducibility of the data. In general, cell lines were verified if 80% of the top 50,000 peaks in one replicate were detected in the top 100,000 peaks of a second replicate. For some cell types, additional verification was performed using similar material hybridized to NimbleGen Human ENCODE tiling arrays (1% of the genome) along with the input DNA as reference (DNase-chip). A more detailed protocol is available here.

The read length for sequences from DNase-seq was 20 bases long due to a MmeI cutting step of the approximately 50 kb DNA fragments extracted after DNaseI digestion. Sequences from each experiment were aligned to the genome using BWA (Li et al., 2008) for the GRCh37 (hg19) assembly.

The command used for these alignments was:
> bwa aln -t 8 genome.fa s_1.sequence.txt.bfq > s_1.sequence.txt.sai
where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format.

Sequences from multiple lanes were combined for a single replicate using the bwa samse command and converted to the sam/bam format using SAMtools.

Only those sequences that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes - see supplemental materials). The mappings of these short reads to the genome are available for download.

Using F-seq, the resulting digital signal was converted to a continuous wiggle track that employs a Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Input data was generated for several cell lines. These were used directly to create a control/background model used for F-Seq when generating signal annotations for these cell lines. These models were meant to correct for sequencing biases, alignment artifacts, and copy number changes in these cell lines. Input data was not generated directly for other cell lines. For cell lines for which there is no input experiment available, the peaks were generated using the control of generic_male or generic_female, as an attempt to create a general background based on input data from several cell types. These files are in "iff" format, which is used when calling peaks with F-seq software, and can be downloaded from the production lab directly from under the section titled "Copy number / karyotype correction." Using a general background model derived from the available Input data sets provided corrections for sequencing biases and alignment artifacts, but did not correct for cell type-specific copy number changes.

The exact command used for this step was:
> fseq -l 600 -v -f 0 -b <bff files> -p <iff files> aligments.bed
where the bff files are the background files based on alignability, the iff files are the background files based on the Input experiments, and alignments.bed is a bed file of filtered sequence alignments.

Discrete DNaseI HS sites (peaks) were identified from DNase-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant.

Data from the high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen were normalized using the Tukey biweight normalization and peaks were called using ChIPOTle (Buck et al., 2005) at multiple levels of significance. Regions matched on size to these peaks that were devoid of any significant signal were also created as a null model. These data were used for additional verification of Tier 1 and Tier 2 cell lines by ROC analysis. Files containing this data can be found in the Downloads directory, labeled 'Validation' in the View column.

Release Notes

This is Release 3 (August 2012) of the track. It includes 27 new experiments including 18 new cell lines.

  • A synthesis of open chromatin evidence from the three assay types was compiled for Tier 1 and 2 cell lines and can be viewed in Open Chromatin Synthesis.
  • Enhancer and Insulator Functional assays: A subset of DNase and FAIRE regions were cloned into functional tissue culture reporter assays to test for enhancer and insulator activity. Coordinates and results from these experiments can be found in the supplemental materials.

Credits

These data and annotations were created by a collaboration of multiple institutions (contact: Terry Furey)

We thank NHGRI for ENCODE funding support.

References

Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 Jun;17(6):910-6.

Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22.

Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8.

Buck MJ, Nobel AB, Lieb JD. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 2005;6(11):R97.

Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503-9.

Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.

Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 Jun;17(6):877-85.

Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Jul;48(3):233-9.

Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Nov;18(11):1851-8.

Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384.

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.