Genome Browser Session Gallery: Difference between revisions

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(New page: {| class="wikitable" border="0"|- |- | == Tier 1 Cell Lines == 400px|thumb|left|Tier 1 cell lines [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&...)
 
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== Tier 1 Cell Lines ==
== ENCODE Tier 1 Cell Lines ==
[[Image:EncodeKent1.gif|400px|thumb|left|Tier 1 cell lines]]
[[Image:EncodeKent1.gif|800px|thumb|none|Tier 1 cell lines]]
[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent1 Launch Browser]     
[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
cell line, and K562, a myeloid line.   The tracks include RNA-seq,
cell line) and K562 (a myeloid line). This track collection includes:
which shows the level of expression of the gene EWSR1, the
* RNA-seq, which shows the level of expression of the gene EWSR1
histone mark H3K4Me, which is associated with promoters, DNAseI
* the histone mark H3K4Me3, which is associated with promoters
hypersensitivity, which is associated with regulatory regions in general,
* 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.)
* ChIP-seq, which shows levels of occupancy by the transcription factor c-­Fos
 
(Contributed by Jim Kent.)




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== Premature Stop in Reference Assembly ==
== Premature Stop in Reference Assembly ==


[[Image:EncodeKent2.gif|400px|thumb|left|Premature stop in reference assembly]]
[[Image:EncodeKent2.gif|800px|thumb|none|Premature stop in reference assembly]]


[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent2 Launch Browser]     
[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent2 Launch Browser]     
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== Multiple Histone Marks ==
== Multiple Histone Marks ==


[[Image:EncodeKent3.gif|400px|thumb|left|Multiple histone marks.]]
[[Image:EncodeKent3.gif|800px|thumb|none|Multiple histone marks.]]


[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent3 Launch Browser]     
[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent3 Launch Browser]     
      
      
All available histone ChIP-seq data on the two Tier 1 cell lines.  
Histone ChIP-seq data on two ENCODE Tier 1 cell lines.  
H3K4me1 is associated with enhancers  and (to an extent) with promoters.  
H3K4me1 is associated with enhancers  and (to an extent) with promoters.  
H3K4me3 is associated with promoters, and H3K36me3 is associated with transcribed regions.
H3K4me3 is associated with promoters, and H3K36me3 is associated with transcribed regions.
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<!-- Commented out til reg tracks are released
== Session from Ross Hardison ==
[[Image:EncodeHardison1.gif|800px|thumb|none]]
BROKEN
[http://genome-test.gi.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Rosshardison&hgS_otherUserSessionName=8q24_9kb_KateR Launch Browser]    -- dang.  this session no longer exists.
(Contributed by Ross Hardison.)
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== Template ==
== Template ==


[[Image:image.jpg|400px|thumb|left|text below image]]
[[Image:image.jpg|600px|thumb|none|text below image]]


[http://urlToSession Launch Browser]     
[http://urlToSession Launch Browser]     
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contributed by .
Contributed by .


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Latest revision as of 23:54, 31 August 2018

ENCODE Tier 1 Cell Lines

Tier 1 cell lines

Launch Browser

Basic ENCODE data on the Tier 1 cell lines GM128 (a lymphoid cell line) and K562 (a myeloid line). This track collection includes:

  • RNA-seq, which shows the level of expression of the gene EWSR1
  • the histone mark H3K4Me3, which is associated with promoters
  • DNAseI hypersensitivity, which is associated with regulatory regions in general
  • ChIP-seq, which shows levels of occupancy by the transcription factor c-­Fos

(Contributed by Jim Kent.)


Premature Stop in Reference Assembly

Premature stop in reference assembly

Launch Browser

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 Browser

Histone ChIP-seq data on two ENCODE Tier 1 cell lines. H3K4me1 is associated with enhancers and (to an extent) with promoters. H3K4me3 is associated with promoters, and H3K36me3 is associated with transcribed regions.


(Contributed by Jim Kent.)


Template

text below image

Launch Browser

Description of scenario.


Contributed by .

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