Genome Browser Session Gallery: Difference between revisions
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== Tier 1 Cell Lines == | == ENCODE Tier 1 Cell Lines == | ||
[[Image:EncodeKent1.gif| | [[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] | ||
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cell line) and K562 (a myeloid line). This track collection includes: | cell line) and K562 (a myeloid line). This track collection includes: | ||
* RNA-seq, which shows the level of expression of the gene EWSR1 | * RNA-seq, which shows the level of expression of the gene EWSR1 | ||
* the histone mark | * the histone mark H3K4Me3, which is associated with promoters | ||
* DNAseI hypersensitivity, which is associated with regulatory regions in general | * DNAseI hypersensitivity, which is associated with regulatory regions in general | ||
* ChIP-seq, which shows levels of occupancy by the transcription factor c-Fos | * ChIP-seq, which shows levels of occupancy by the transcription factor c-Fos | ||
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== Premature Stop in Reference Assembly == | == Premature Stop in Reference Assembly == | ||
[[Image:EncodeKent2.gif| | [[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| | [[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] | ||
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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== Session from Ross Hardison == | == Session from Ross Hardison == | ||
[[Image:EncodeHardison1.gif|800px|thumb|none]] | [[Image:EncodeHardison1.gif|800px|thumb|none]] | ||
BROKEN | |||
[http://genome-test. | [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.) | (Contributed by Ross Hardison.) | ||
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== Template == | == Template == | ||
Latest revision as of 23:54, 31 August 2018
ENCODE Tier 1 Cell LinesBasic ENCODE data on the Tier 1 cell lines GM128 (a lymphoid cell line) and K562 (a myeloid line). This track collection includes:
(Contributed by Jim Kent.)
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Premature Stop in Reference AssemblyA 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.
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Multiple Histone MarksHistone 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.
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TemplateDescription of scenario.
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