DNase Clusters item details
  Items in Cluster: 52 of 95
Cluster Score (out of 1000): 739
Position: chr10:96142361-96142630
Band: 10q24.1
Genomic Size: 270
View DNA for this feature (hg38/Human)

List of Items in Cluster
 
#signalcellTypetreatmentmore info
112.00A549 wgEncodeRegDnaseUwA549Peak
268.00AG04449 wgEncodeRegDnaseUwAg04449Peak
339.00AG04450 wgEncodeRegDnaseUwAg04450Peak
444.00AG09309 wgEncodeRegDnaseUwAg09309Peak
517.00AG09319 wgEncodeRegDnaseUwAg09319Peak
619.00AG10803 wgEncodeRegDnaseUwAg10803Peak
711.00AoAF wgEncodeRegDnaseUwAoafPeak
821.00BJ wgEncodeRegDnaseUwBjPeak
974.00bone_marrow_MSC wgEncodeRegDnaseUwBonemarrowmscPeak
1045.00GM04503 wgEncodeRegDnaseUwGm04503Peak
1137.00GM04504 wgEncodeRegDnaseUwGm04504Peak
129.00HA-h wgEncodeRegDnaseUwHahPeak
1338.00HA-sp wgEncodeRegDnaseUwHaspPeak
1449.00HAEpiC wgEncodeRegDnaseUwHaepicPeak
1551.00HBMEC wgEncodeRegDnaseUwHbmecPeak
1610.00HBVSMC wgEncodeRegDnaseUwHbvsmcPeak
1728.00HCF wgEncodeRegDnaseUwHcfPeak
1842.00HCFaa wgEncodeRegDnaseUwHcfaaPeak
1925.00HCM wgEncodeRegDnaseUwHcmPeak
2020.00HConF wgEncodeRegDnaseUwHconfPeak
2177.00HCPEpiC wgEncodeRegDnaseUwHcpepicPeak
2214.00HEEpiC wgEncodeRegDnaseUwHeepicPeak
2328.00HFF wgEncodeRegDnaseUwHffPeak
248.00HFF-Myc wgEncodeRegDnaseUwHffmycPeak
2539.00HGF wgEncodeRegDnaseUwHgfPeak
26106.00HIPEpiC wgEncodeRegDnaseUwHipepicPeak
2722.00HL-60 wgEncodeRegDnaseUwHl60Peak
2811.00HMEC wgEncodeRegDnaseUwHmecPeak
2936.00HMF wgEncodeRegDnaseUwHmfPeak
3067.00HNPCEpiC wgEncodeRegDnaseUwHnpcepicPeak
3120.00HPAF wgEncodeRegDnaseUwHpafPeak
3251.00HPdLF wgEncodeRegDnaseUwHpdlfPeak
3311.00HPF wgEncodeRegDnaseUwHpfPeak
3412.00HRE wgEncodeRegDnaseUwHrePeak
3512.00HRPEpiC wgEncodeRegDnaseUwHrpepicPeak
3675.00HSMM wgEncodeRegDnaseUwHsmmPeak
3724.00HSMMtube wgEncodeRegDnaseUwHsmmtubePeak
3811.00HVMF wgEncodeRegDnaseUwHvmfPeak
397.00K562 wgEncodeRegDnaseUwK562Peak
4075.00LHCN-M2 wgEncodeRegDnaseUwLhcnm2Peak
4124.00LHCN-M2 DIFF_4d wgEncodeRegDnaseUwLhcnm2Diff4dPeak
4211.00Monocytes-CD14+_RO01746 wgEncodeRegDnaseUwMonocytescd14ro01746Peak
4322.00NH-A wgEncodeRegDnaseUwNhaPeak
4452.00NHDF-Ad wgEncodeRegDnaseUwNhdfadPeak
4519.00NHDF-neo wgEncodeRegDnaseUwNhdfneoPeak
4613.00NHEK wgEncodeRegDnaseUwNhekPeak
4730.00NHLF wgEncodeRegDnaseUwNhlfPeak
4816.00RPTEC wgEncodeRegDnaseUwRptecPeak
498.00SAEC wgEncodeRegDnaseUwSaecPeak
5013.00SK-N-MC wgEncodeRegDnaseUwSknmcPeak
5173.00SKMC wgEncodeRegDnaseUwSkmcPeak
5210.00WI-38 wgEncodeRegDnaseUwWi38Peak
List all items assayed

Track Description
 
View table: schema,

Go to DNase Clusters track controls

Data last updated: 2019-01-08


p12 Note: includes annotations on GRCh38.p12 patch sequences

Description

This track shows clusters of DNaseI hypersensitivity derived from assays in 95 cell types by the John Stamatoyannapoulos lab at the University of Washington from September 2007 to January 2011, as part of the ENCODE project first production phase. Regulatory regions in general, and promoters in particular, tend to be DNase-sensitive.

Additional views of this data sites are displayed from the DNaseI HS track. The peaks in that track are the basis for the clusters shown here, which combine data from peaks from the different cell lines. Please note that track colors for the DNase tracks are based on similiarity of cell types, while there is different coloring for cell types on the ENCODE hg38 Transcription track, Layered H3K4Me1 track, Layered H3K4Me3 track, and Layered H3K27Ac track, which match the coloring used in their previous versions lifted from the hg19 assembly.

Display Conventions and Configuration

A gray box indicates the extent of the hypersensitive region. The darkness is proportional to the maximum signal strength observed in any cell line. The number to the left of the box shows how many cell lines are hypersensitive in the region. The track can be configured to restrict the display to elements above a specified score in the range 1-1000 (where score is based on signal strength).

Methods

Raw sequence data files were processed by the UCSC ENCODE DNase analysis pipeline (July 2014 specification), diagrammed here:

ENCODE DNase Pipeline Credit: Qian Alvin Qin, X. Liu lab

Briefly, sequence files were aligned to the hg38 (GRCh38) genome assembly augmented with 'sponge' sequence (ref). Multi-mapped reads were removed, as were reads that aligned to 'sponge' or mitochondiral sequence. Results from all replicates were pooled, and further processed by the Hotspot program to call peaks.

Peaks of DNaseI hypersensitivity from the ENCODE DNase Analysis Pipeline at UCSC were assigned normalized scores (by UCSC regClusterMakeTableOfTables) in the range 0-1000 based on the narrowPeak signalValue and then clustered on score (by UCSC regCluster) to generate singly-linked clusters. Additional documentation on the methods used to identify hypersensitive sites are available from the DNaseI HS track.

Credits

This track is based on sequence data from the University of Washington ENCODE group, with subsequent processing by UCSC. For additional credits and references, see the DNaseI HS track.