Genome Browser Session Gallery: Difference between revisions

Revision as of 20:38, 13 July 2010

Contents 1 Tier 1 Cell Lines 2 Premature Stop in Reference Assembly 3 Multiple Histone Marks 4 Template 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 H3K4Me, 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 All available histone ChIP-seq data on the two 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 .

@@ Line 6: / Line 6: @@
 [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 H3K4Me, 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.)