Maps of the Saccharomyces Genome

Publication: Genome-wide structure and organization of eukaryotic pre-initiation complexes. by Rhee HS, and Pugh BF Nature (2012 Jan 18)

Publication: Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution by Rhee HS, and Pugh BF Cell (2011 Dec 9)

Supplementary Data Raw Sequencing Data.

Publication: Genome-wide function of H2B ubiquitylation in promoter and genic regions by Kiran Batta, Zhenhai Zhang, Kuangyu Yen, David B. Goffman, and B. Franklin Pugh Genes Dev. (2011 Nov 1)

Supplementary Data Sequencing Data.

Publication: Stable and dynamic nucleosome states during a meiotic developmental process by Zhang L, Ma H, and Pugh BF Genome Res. (2011 Jun)

Download sequencing data in Genetrack format H3, H3K4me3, H3K9ac, H3K36me3, H3K79me3

Download reference genome saccharomyces_cerevisiae-JAN-19-2007

More information about GeneTrack

Publication: A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. by Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, and B. Franklin Pugh Science. (2011 May 20)

Supplementary Data Download: 20090513, 20090825(SGD, ATP, FULL, 4C, 37C), 20100108, 20100130, 20101012

Genetrack index files: tag_index

Publication: A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces by Venters BJ, Wachi S, Mavrich TN, Andersen BE, Jena P, Sinnamon AJ, Jain P, Rolleri NS, Jiang C, Hemeryck-Walsh C and B. Franklin Pugh Mol Cell. (2011 Feb 18)

Download the supplementary data on occupancy

Publication: High-resolution genome-wide mapping of the primary structure of chromatin. by Zhang Z, and B. Franklin Pugh Cell. (2011 Jan 21)

Publication: Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae. by Ghosh S, and B. Franklin Pugh Mol Cell Biol. (2011 Jan)

Download the supplementary information (Table 1 and Table 2)

Publication: Genome-Wide Transcriptional Dependence on Conserved Regions of Mot1 by Bryan J. Venters, Jordan D. Irvin, Paul Gramlich, and B. Franklin Pugh

Supplementary data mot1-supp-data.zip (1.2Mb).

Publication: A systematic reference map of nucleosome positions across the Saccharomyces genome Cizhong Jiang and B. Franklin Pugh

Nucleosome browsers:

• Retrieval system to extract reference nucleosome positions.
• Assigning newly measured nucleosome positions to a reference

Publication: Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome R. Thomas Koerber, Ho Sung Rhee,, Cizhong Jiang and B. Franklin Pugh Molecular Cell, Volume 35, Issue 6, 889-902, 24 September 2009

Download the interaction data.

Publication: A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome Travis N. Mavrich, Ilya P. Ioshikhes, Bryan J. Venters, Cizhong Jiang, Lynn P. Tomsho, Ji Qi, Stephan C. Schuster, Istvan Albert, and B. Franklin Pugh Genome Research, published online June 12, 2008

Download the H3H4 sequencing data . Visit the H3H4 browser (now combined with the H2AZ nucleosomal data) displaying the nucleosome predictions. More information about GeneTrack a custom software tool written to address the storage, analysis and display needs of our project.

Publication: Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome Istvan Albert, Travis N. Mavrich, Lynn P. Tomsho, Ji Qi, Sara J. Zanton , Stephan C. Schuster, and B. Franklin Pugh Nature 446, 572-576, (2007)

Download the H2AZ sequencing data. Visit the H2AZ browser (now combined with the H3/H4 data) displaying the nucleosome predictions. More information about GeneTrack a custom software tool written to address the storage, analysis and display needs of our project.

Publication: Nucleosome positions predicted by comparative genomics Ilya P. Ioshikhes, Istvan Albert, Sara J. Zanton, and B. Franklin Pugh Nature Genetics - 38 , 1210-1215 (2006)

Download the correlation data. Visit the correlation browser displaying the nucleosome predictions based on the dinucleotide correlation pattern.