Open Access Highly Accessed Methodology article

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

Philippe Lefrançois1, Ghia M Euskirchen1, Raymond K Auerbach2, Joel Rozowsky3, Theodore Gibson3, Christopher M Yellman1, Mark Gerstein23 and Michael Snyder123*

Author Affiliations

1 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA

2 Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA

3 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA

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BMC Genomics 2009, 10:37  doi:10.1186/1471-2164-10-37

Published: 21 January 2009

Additional files

Additional file 1:

Cse4 target lists. This data correspond to the annotated filtered target lists and the raw 'hits' returned from PeakSeq for three biological replicates of Cse4 ChIP DNA processed by ChIP-Seq.

Format: XLS Size: 220KB Download file

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Additional file 2:

Ste12 target lists. This data correspond to the annotated filtered target lists and the raw 'hits' returned from PeakSeq for three biological replicates of Ste12 ChIP DNA processed by ChIP-Seq.

Format: XLS Size: 958KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

PolII target lists. This data correspond to the annotated filtered target lists and the raw 'hits' returned from PeakSeq for four biological replicates of PolII ChIP DNA processed by ChIP-Seq.

Format: XLS Size: 3.6MB Download file

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Additional file 5:

Complete GO analysis for Cse4, Ste12 and PolII. This data represent the complete GO process analysis for Cse4 combined targets, Ste12 combined targets and PolII combined targets, with a p-value cutoff < 0.01.

Format: XLS Size: 173KB Download file

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Additional file 4:

Sequencing artifacts present in non-barcoded samples and absent in barcoded samples. These IGB signal tracks show abnormally-shaped peaks present in non-barcoded biological replicates at a particular genomic location that are absent in barcoded biological replicates.

Format: PDF Size: 329KB Download file

This file can be viewed with: Adobe Acrobat Reader

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