Encode scenarios

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Tier 1 Cell Lines

Tier 1 cell lines

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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

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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.

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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

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Description of scenario.


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