Open Access Highly Accessed Research article

Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes

Henriette O'Geen1, Yu-Hsuan Lin23, Xiaoqin Xu1, Lorigail Echipare1, Vitalina M Komashko1, Daniel He1, Seth Frietze1, Osamu Tanabe2, Lihong Shi2, Maureen A Sartor3, James D Engel2 and Peggy J Farnham1*

Author Affiliations

1 Genome Center, University of California at Davis, Davis, CA 95616, USA

2 Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA

3 Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA

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BMC Genomics 2010, 11:689  doi:10.1186/1471-2164-11-689

Published: 2 December 2010

Additional files

Additional file 1:

Validation of TR4 expression in four different cell types. Western blot analysis to validate expression of TR4 protein. 10 μg nuclear extract were loaded per lane. Cell types used are indicated above each lane.

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Additional file 2:

Primer sequences for standard and qPCR validation of TR4 ChIP samples.

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Additional file 3:

PCR anaslysis of three TR4 binding sites. ChIP assays were performed in K562 and HepG2 cells using TR4 antibody. PCR was performed using primers to TR4 binding sites identified by ChIP-seq (see Additional file 2 for oligo sequences). The enrichment of TR4 is shown in comparison to 0.1% Input chromatin. IgG ChIPs were used as negative controls. PCR analysis confirmed presence of TR4 at TNFIAP1, ECSIT and SCAP, but showed no significant enrichment when using negative control primers to ZNF333.

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Additional file 4:

ChIP-seq data and analysis summary

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