ENCODE Regulation Transcription Track Settings
Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE

Track collection: Integrated Regulation from ENCODE

+  Description
+  All tracks in this collection (8)

Display mode:       Reset to defaults

Overlay method:
Type of graph:
Track height: pixels (range: 11 to 100)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 65535)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
 Select all subtracks
List subtracks: only selected/visible    all    ()    Restricted Until 
      GM12878  Transcription of GM12878 cells from ENCODE    Schema   2011-10-21 
      H1-hESC  Transcription of H1-hESC cells from ENCODE    Schema   2011-10-21 
      HeLa-S3  Transcription of HeLa-S3 cells from ENCODE    Schema   2010-10-12 
      HepG2  Transcription of HepG2 cells from ENCODE    Schema   2010-10-11 
      HSMM  Transcription of HSMM cells from ENCODE    Schema   2011-10-21 
      HUVEC  Transcription of HUVEC cells from ENCODE    Schema   2011-10-21 
      K562  Transcription of K562 cells from ENCODE    Schema   2011-10-21 
      NHEK  Transcription of NHEK cells from ENCODE    Schema   2011-10-21 
      NHLF  Transcription of NHLF cells from ENCODE    Schema   2011-10-21 


This track shows transcription levels for several cell types as assayed by high-throughput sequencing of polyadenylated RNA (RNA-seq). Additional views of this dataset and additional documentation on the methods used for this track are available at the ENCODE Caltech RNA-seq page. The data shown here are derived from the Raw Signal view from the paired 75-mer 200 bp insert size reads. The two replicates of the signal were pooled and normalized so that the total genome-wide signal sums to 10 billion.

Display Conventions and Configuration

By default, this track uses a transparent overlay method of displaying data from a number of cell lines in the same vertical space. Each of the cell lines in this track is associated with a particular color and these cell line colors are consistent across all tracks that are part of the ENCODE Regulation supertrack. These colors are relatively light and saturated so as to work best with the transparent overlay. Unfortunately, outside the ENCODE Regulation tracks, older cell line color conventions are used that don't match the cell line colors used in the ENCODE Regulation tracks. The older colors were not used in the ENCODE Regulation tracks because they were too dark for the transparent overlay.


This track shows data from the Wold Lab at Caltech, as part of the ENCODE Project Consortium.

Release Notes

This is release 2 (July 2012) of this track which includes two new subtracks for HeLa-S3 and HepG2.

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.