Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro

Sumantra Chatterjee; Petra Kraus; V Sivakamasundari; Sook Peng Yap; Vibhor Kumar; Shyam Prabhakar; Thomas Lufkin

doi:10.1016/j.gdata.2016.09.002

Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro

Genom Data. 2016 Sep 8:10:51-3. doi: 10.1016/j.gdata.2016.09.002. eCollection 2016 Dec.

Authors

Sumantra Chatterjee¹, Petra Kraus², V Sivakamasundari³, Sook Peng Yap⁴, Vibhor Kumar⁵, Shyam Prabhakar⁵, Thomas Lufkin²

Affiliations

¹ McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
² Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA.
³ The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA.
⁴ Apta Biosciences, 31 Biopolis Way, Nanos, Singapore 138669, Singapore.
⁵ Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.

Abstract

This work pertains to GEO submission GSE36672, in vivo and in vitro genome wide binding (ChIP-Seq) of Bapx1/Nkx3.2 and Sox9 proteins. We have previously shown that data from a genome wide binding assay combined with transcriptional profiling is an insightful means to divulge the mechanisms directing cell type specification and the generation of tissues and subsequent organs [1]. Our earlier work identified the role of the DNA-binding homeodomain containing protein Bapx1/Nkx3.2 in midgestation murine embryos. Microarray analysis of EGFP-tagged cells (both wildtype and null) was integrated using ChIP-Seq analysis of Bapx1/Nkx3.2 and Sox9 DNA-binding proteins in living tissue.

Keywords: Bapx1; ChIP-Seq; Genome binding; Mouse; Occupancy profiling by NGS.