TSUKIYAMA LAB -- global_nucleosome_mapping
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Global Nucleosome Mapping

Data files for Whitehouse et al., 2007

Note about nucleosomes: Nucleosomes are called by iteratively fitting an idealized nucleosome signal to the data. Signals with the best fit are designated as positioned nucleosomes. Bear in mind that this technique will generally NOT detect highly delocalized (fuzzy) nucleosomes. Please do not interpret regions without positioned nucleosomes as being nucleosome free!

View the processed data with the UCSC genome browser:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=sacCer1&position= chr9:40,065-43,826&hgt.customText=http://labs.fhcrc.org/tsukiyama/supplemental_data/global_nucleosome_mapping/whitehouse_bedfiles.txt

.bed files:

Whitehouse_Bedfiles.txt

Processed data is listed below. It is tab delimited text and can be viewed directly using IGB which is available from http://www.affymetrix.com/support/developer/tools/download_igb.affx (free registration required). Each file is ~60Mb.

For PC, right click on the link to Save Target As... on your computer

For MAC, click on link + Control and Download Linked File to your Mac

Files need the extension .sgr (not .txt) to be opened with IGB

1. Nucleosome positioning data: chromosome : position (bp) : value (log2)
•  WT nucleosome positions  File: WT_nucs.sgr (zipped)
•  Δisw2 nucleosome positions File: isw2_nucs.sgr (zipped)

2. Chromatin remodeling data: chromosome : position (bp) : value (a.u.)
•    File: Chr_remodelling.sgr (zipped)

3. Isw2-K215R enrichment data: chromosome : position (bp) : value (log2)
•    File: Isw2_ChIP.sgr (zipped)

Raw data (Cel files) are available from GEO with accession numbers GSE8813, GSE8814, and GSE8815

 

Last updated: 11/28/07