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ENC Exon Array UW Affy Exon Track Settings
 
Affymetrix Exon Array from ENCODE/University of Washington

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 All Treatment None  4-OHTAM 20 nM 72 hr  Differentiated 2 d  Differentiated 5 d  Differentiated 9 d  Differentiated 14 d 
Cell Line
GM12878 (Tier 1) 
K562 (Tier 1) 
A549 (Tier 2) 
HeLa-S3 (Tier 2) 
HepG2 (Tier 2) 
HUVEC (Tier 2) 
MCF-7 (Tier 2) 
AG04449 
AG04450 
AG09309 
AG09319 
AG10803 
AoAF 
BE2 C 
BJ 
Caco-2 
CMK 
GM06990 
GM12864 
GM12865 
H7-hESC 
HAc 
HAEpiC 
HA-h 
HA-sp 
HBMEC 
HBVP 
HBVSMC 
HCF 
HCFaa 
HCM 
HConF 
HCPEpiC 
HCT-116 
HEEpiC 
HEK293 
HFF 
HFF-Myc 
HGF 
HIPEpiC 
HL-60 
HMEC 
HMF 
HMVEC-dAd 
HMVEC-dBl-Ad 
HMVEC-dBl-Neo 
HMVEC-dLy-Ad 
HMVEC-dLy-Neo 
HMVEC-dNeo 
HMVEC-LBl 
HMVEC-LLy 
HNPCEpiC 
HPAEC 
HPAF 
HPdLF 
HPF 
HRCEpiC 
HRE 
HRGEC 
HRPEpiC 
HSMM 
HSMMtube 
HVMF 
Jurkat 
LNCaP 
NB4 
NH-A 
NHBE 
NHDF-Ad 
NHDF-neo 
NHEK 
NHLF 
NT2-D1 
PANC-1 
PrEC 
RPTEC 
SAEC 
SkMC 
SK-N-MC 
SK-N-SH RA 
Th1 
WERI-Rb-1 
WI-38 
Cell Line
 All Treatment None  4-OHTAM 20 nM 72 hr  Differentiated 2 d  Differentiated 5 d  Differentiated 9 d  Differentiated 14 d 
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  Cell Line↓1 Rep↓2   Track Name↓3    Restricted Until↓4
 
Dense
 GM12878  1  GM12878 Exon array Signal Rep 1 from ENCODE/UW    Data format   2010-06-21 
 
Dense
 K562  1  K562 Exon array Signal Rep 1 from ENCODE/UW    Data format   2010-04-02 
 
Dense
 K562  2  K562 Exon array Signal Rep 2 from ENCODE/UW    Data format   2010-06-21 
     Restriction Policy
Assembly: Human Feb. 2009 (GRCh37/hg19)

Description

This track displays human tissue microarray data using Affymetrix Human Exon 1.0 GeneChip and was produced as part of the ENCODE Project. This track in the hg19 assembly is a continuation of the work displayed in the hg18 assembly with additional cell lines.

Display Conventions and Configuration

The display for this track shows probe location and signal value as grayscale-colored items where higher signal values correspond to darker-colored blocks. Items with score of 1000 are in the highest 10% quantile for signal value of that particular cell type. Similarly, items scoring 900 are the next 10% quantile and at the bottom of scale, items scoring 100 are in the lowest 10% quantile for signal value.

The subtracks within this composite annotation track correspond to data from different cell types and tissues. The configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide.

For information regarding specific microarray probes, look under the "Expression" track group and turn on the Affy Exon Array track.

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. A subset of the cells were stored frozen in RNAlater. For the WI-38 Tamoxifen-treated (4OHTAM_20nM_72hr) cell type, cells at 50-80% confluency were treated for 72 hours with 20 nM 4-hydroxytamoxifen in growth medium (from a 1000X working stock in absolute ethanol). At harvest, greater than 95% of DNA synthesis was inhibited and the cells had an induced fusiform/round morphology with greater than 95% showing dramatic senescence-associated heterochromatic foci. Total RNA was labeled and hybridized to Affymetrix Human Exon 1.0 ST V2 arrays using hg19 probesets. Exon and gene level expression analysis were carried out using Affymetrix ExACT 1.2.1 and Affymetrix Expression Console 1.1 software tools. Samples were quantile normalized for background correction and Probe Logarithmic Intensity Error summarized. More detailed methods are here.

Release Notes

This is release 4 (Jul 2012) of this track. A patch update has removed previously released K562 zinc-finger experiments due to a data merging issue. This update adds in H7-hESC cells that have been differentiated with different time courses.

Verification

Data were verified by sequencing biological replicates displaying correlation coefficient of 0.9 or greater.

Credits

These data were generated by the University of Washington ENCODE group.

Contact: Richard Sandstrom

References

Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44.

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.