Encode scenarios: Difference between revisions

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== Tier 1 Cell Lines ==
== Tier 1 Cell Lines ==
 
[[Image:EncodeKent1.gif|400px|thumb|left|Tier 1 cell lines]]
[[Image:EncodeKent1.jpg|400px|thumb|left|Tier 1 cell lines]]
[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent1 Launch active Browser at this location]     
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent1 Launch Browser]     
      
      
Basic ENCODE data on the Tier 1 cell lines GM128, a lymphoid
Basic ENCODE data on the Tier 1 cell lines GM128, a lymphoid
Line 9: Line 10:
which shows the level of expression of the gene EWSR1, the
which shows the level of expression of the gene EWSR1, the
histone mark, H3K4Me, which is associated with promoters; DNAseI
histone mark, H3K4Me, which is associated with promoters; DNAseI
hypersensitivity, which is associated with regulatory regions in general; and ChIP-seq showing levels of occupancy by the transcription factor c-­Fos.
hypersensitivity, which is associated with regulatory regions in general;  
and ChIP-seq showing levels of occupancy by the transcription factor c-­Fos.
 
contributed by Jim Kent.
 
 
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== Premature Stop in Reference Assembly ==


[[Image:EncodeKent2.gif|400px|thumb|left|Premature stop in reference assembly]]
[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent2 Launch active Browser at this location]   
   
A premature stop codon that is found in the reference genome and about half of people of European descent.  The UCSC Genes track is forced to skip the codon.
contributed by Jim Kent.
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== Multiple Histone Marks ==
[[Image:EncodeKent3.gif|400px|thumb|left|Multiple histone marks.]]
[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent3 Launch active Browser at this location]   
   
All available histone ChIP-seq data on the two tier one cell lines.
H3K4me1 is associated with enhancers  and to an extent with promoters,
H3K4me3 with promoters, and H3K36me3 with transcribed regions.
contributed by Jim Kent.
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== Template ==
== Template ==


[[Image:image.jpg|400px|thumb|left|text below image]]
[[Image:image.jpg|400px|thumb|left|text below image]]


[http://urlToSession Launch Browser]     
[http://urlToSession Launch active Browser at this location]     
      
      
Description of scenario.
Description of scenario.


[[Category: Encode]]
 
contributed by .
 
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Latest revision as of 17:40, 12 April 2010

Tier 1 Cell Lines

Tier 1 cell lines

Launch active Browser at this location

Basic ENCODE data on the Tier 1 cell lines GM128, a lymphoid cell line and K562, a myeloid line. The tracks include RNA-­seq which shows the level of expression of the gene EWSR1, the histone mark, H3K4Me, which is associated with promoters; DNAseI hypersensitivity, which is associated with regulatory regions in general; and ChIP-seq showing levels of occupancy by the transcription factor c-­Fos.

contributed by Jim Kent.


Premature Stop in Reference Assembly

Premature stop in reference assembly

Launch active Browser at this location

A premature stop codon that is found in the reference genome and about half of people of European descent. The UCSC Genes track is forced to skip the codon.


contributed by Jim Kent.

Multiple Histone Marks

Multiple histone marks.

Launch active Browser at this location

All available histone ChIP-seq data on the two tier one cell lines. H3K4me1 is associated with enhancers and to an extent with promoters, H3K4me3 with promoters, and H3K36me3 with transcribed regions.


contributed by Jim Kent.

Template

text below image

Launch active Browser at this location

Description of scenario.


contributed by .