Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells

Published: 01-07-2019| Version 2 | DOI: 10.17632/s23bhg4xjv.2
Contributors:
Banushree Kumar,
Simon Elsässer

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Various supplementary data, information and pseudocode

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Kumar_2019_GeneSets_Promoters.mm9.bed Bivalent gene set in mouse ESC were from Mikkelsen et. al. (2007). Low, medium and high expressed gene sets are representative of the top, middle and bottom quantile of transcription in Serum/LIF grown ESC, derived from TT-Seq data. Promoters are defined as regions +/- 1kb from TSS of each gene. genes_biv_up and genes_biv_down designate gene sets that were found to have an gain or loss of histone H3K27me3 levels in the promoter region in 2i condition over Serum condition, each represents the union of differentially methylated promoters (>1.5fold change) from independent biological experiments with three different H3K27me3 antibodies.