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ENCODE 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). 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

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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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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.)


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Description of scenario.

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