Pokholok_2005_PMID_16122420.README
Last modified: 2016-06-16

Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell
GW, Walker K, Rolfe PA, Herbolsheimer E, Zeitlinger J, Lewitter F,
Gifford DK, Young RA (2005) Genome-wide map of nucleosome acetylation
and methylation in yeast. Cell 122(4):517-27
PMID: 16122420

Pokholok et al. performed ChIP-chip assays to examine the distribution
of methylated and acetylated histones in modififed nucleosomes across
the budding yeast genome.

A short summary of the contents of each data file compiled by SGD can
be found in the following section. More in depth details can be found
within the file header of each file.

Data files last modified: June 28, 2011
SGD has compiled the following data files from this publication:

* Pokholok_2005_histone_H3_vs_WCE_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3_vs_WCE_H2O2_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K9ac_vs_H3_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K14ac_vs_H3_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K14ac_vs_H3_H2O2_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K14ac_vs_WCE_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K4me1_vs_H3_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K4me2_vs_H3_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K4me3_vs_H3_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K36me3_vs_H3_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H3K79me3_vs_H3_YPD_ChIP_chip.bedgraph

* Pokholok_2005_histone_H4_vs_WCE_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H4ac_vs_H3_YPD_ChIP_chip.bedgraph
* Pokholok_2005_histone_H4ac_vs_H3_H2O2_ChIP_chip.bedgraph

* Pokholok_2005_ESA1_vs_WCE_YPD_ChIP_chip.bedgraph
* Pokholok_2005_GCN5_vs_WCE_YPD_ChIP_chip.bedgraph
* Pokholok_2005_GCN4_vs_WCE_AA_ChIP_chip.bedgraph

* Pokholok_2005_IgG_control_YPD_ChIP_chip.bedgraph
* Pokholok_2005_no_antibody_control_YPD_ChIP_chip.bedgraph

These data files were compiled using the file
"Pokholok_et_al_data.xls" supplied by the authors at their
supplementary website:

http://younglab.wi.mit.edu/nucleosome/DataDownload.html

containing the average ratio of immunoprecipitated to control DNA for
each microarray spot across all replicates for each of the
modifications/factors/conditions listed above.


Additional supplementary information:

ArrayExpress accession: E-WMIT-3
http://www.ebi.ac.uk/arrayexpress/experiments/E-WMIT-3/

http://web.wi.mit.edu/young/nucleosome/