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Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis

Hai Wu1, Troy W Whitfield2, Jonathan A R Gordon1, Jason R Dobson34, Phillip W L Tai1, Andre J van Wijnen5, Janet L Stein1, Gary S Stein1 and Jane B Lian1*

Author Affiliations

1 Department of Biochemistry, University of Vermont College of Medicine and Vermont Cancer Center, 89 Beaumont Avenue, Burlington, VT 05405, USA

2 Department of Cell & Developmental Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01655, USA

3 Current address: Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, 115 Waterman Street, Providence, RI 02912, USA

4 Current address: Department of Computer Science, Brown University, 115 Waterman Street, Providence, RI 02912, USA

5 Current address: Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Medical Sciences Building 3-69, 200 First Street SW, Rochester, MN 55905, USA

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Genome Biology 2014, 15:R52  doi:10.1186/gb-2014-15-3-r52

Published: 21 March 2014

Additional files

Additional file 1: Table S3:

Summary of MC3T3 Runx2 ChIP-Seq. This table lists the read numbers and genome coverage of Runx2 ChIP-Seq libraries.

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Additional file 2: Table S4:

Distribution patterns of Runx2 peaks across genomic locations. This table is related to Figure 2.

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Additional file 3:

Detailed description of ChIP-PCR, ChIP-Seq with bioinformatics analysis, and supplemental figure legends.

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Additional file 4: Table S5:

GREAT Gene Ontology terms. This table contains the top GO terms assigned by GREAT to clusters 1 to 7 defined in Figure 3A.

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Additional file 5: Figure S1:

GO term analysis from GREAT for clusters 1 to 3 and 5 to 7 in Figure 3A. This is related to Figure 3.

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Additional file 6: Figure S8:

Validation of Runx2 peaks by ChIP-PCR. This figure is related to Figures 4, 5 and 6.

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Additional file 7: Figure S2:

Runx2 peaks associated with Bsp gene during differentiation. This figure is related to Figure 4.

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Additional file 8: Table S6:

Detailed annotation of Runx2 peaks. This table is a meta-spreadsheet of Runx2 peaks annotated to RefSeq genes.

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Additional file 9: Figure S3:

Validation of Runx2 knockdown in MC3T3 cells. This figure is related to Figure 5.

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Additional file 10: Figure S4:

Additional characteristics of Runx2 binding in shRunx2 responsive genes. This figure is related to Figure 5.

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Additional file 11: Figure S5:

PeaksToGenes analysis of Runx2 occupancy in Runx2 shRNA-responsive genes. This figure is related to Figure 5E.

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Additional file 12: Figure S6:

EMBER analyses of Runx2 binding in the genes differentially regulated by Runx2 knockdown. This figure is related to Figure 5.

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Additional file 13: Figure S7:

Validation of novel Runx2 target Tnfrsf19. This figure is related to Figure 6.

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Additional file 14: Table S7:

Genes responsive to Runx2 shRNA. This table lists the genes that are up- or down- regulated by shRunx2 treatment in MC3T3 cells differentiated for 9 days.

Format: XLSX Size: 27KB Download file

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Additional file 15: Table S1:

qPCR and ChIP-PCR primers.

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Additional file 16: Table S2:

Cloning primers. This table contains the primers used for plasmid construction.

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