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 (9)

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    ()  
      GM12878  Transcription of GM12878 cells from ENCODE   Data format 
      H1-hESC  Transcription of H1-hESC cells from ENCODE   Data format 
      HeLa-S3  Transcription of HeLa-S3 cells from ENCODE   Data format 
      HepG2  Transcription of HepG2 cells from ENCODE   Data format 
      HSMM  Transcription of HSMM cells from ENCODE   Data format 
      HUVEC  Transcription of HUVEC cells from ENCODE   Data format 
      K562  Transcription of K562 cells from ENCODE   Data format 
      NHEK  Transcription of NHEK cells from ENCODE   Data format 
      NHLF  Transcription of NHLF cells from ENCODE   Data format 
Assembly: Human Dec. 2013 (GRCh38/hg38)
Data coordinates converted via liftOver from: Feb. 2009 (GRCh37/hg19)

Note: lifted from hg19


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 colors are relatively light and saturated so as to work best with the transparent overlay. The color of these tracks match their versions from their lifted source on the hg19 assembly. The colors are consistent with the other hg19 lifted tracks located in the ENCODE Regulation supertrack, with the exception being the DNase tracks, as they were not lifted from hg19 and are colored to reflect similarity of cell types.


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

Primary ENCODE data produced during the 2007-2012 production phase were subject to a restriction period. However, the data here are past those restrictions and are freely available. The full data release policy for ENCODE is available here.