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Open Access Research article

Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods

Fan Gao12, Zong Wei1, Wange Lu1* and Kai Wang2*

Author Affiliations

1 Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA

2 Zilkha Neurogenetic Institute, Department of Psychiatry and Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA

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BMC Genomics 2013, 14:345  doi:10.1186/1471-2164-14-345

Published: 24 May 2013

Additional files

Additional file 1:

Summary of mapping results of 4C-Seq data.

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Additional file 2: Figure S1:

Distribution of read counts at all inter-chromosomal interaction sites. Data generated from the biological replicates BR1 and BR2 were compared. Both enzyme-based and sonication-based data were included in the plots.

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Additional file 3: Figure S2:

Reproducibility of inter-chromosomal interactions at different resolutions. Density scatter plots of inter-chromosomal interactions between the biological replicate data at resolutions of (A),1 Mb for sonication-based data; (B), 250 6-bp cutter sites for enzyme-based data; (C), 500 kb for sonication-based data; (D), 125 6-bp cutter sites for enzyme-based data.

Format: TIFF Size: 107KB Download file

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