Project name: Homo sapiens

Description: Evidence for the epigenetic regulation of hematopoietic stem cells (HSCs) is growing, but the genome-wide epigenetic signature of HSCs and its functional significance remain unclear. In this study, we used high-resolition (Agilent, CpG Island ChIP-on-chip) platforms for genome-wide comparison of CpG methylation in human CD34+ and CD34- cells.Overall design: CD34+ and CD34- cells were purified from human umbilical cord blood. Genomic DNA obtained from CD34+ and CD34- cells was fragmented by either sonication or digestion with MseI. Recombinant methyl-binding domain (Genomictree, Daejeon, Korea) was incubated with sonicated genomic DNA in a binding reaction mixture. The methyl-enriched DNA fraction was purified using Qiaquick PCR purification kits (Qiagen, Hilden, Germany) and amplified using a whole genome amplification kit as recommended by Agilent. Amplified DNA products from CD34+ and CD34- cells were labeled with Cy3-dUTP and Cy5-dUTP, respectively, by random priming and hybridized onto Agilent human CpG island microarrays using conditions specified by the manufacturer (Agilent, Santa Clara, CA). After washing, the slides were scanned using an Agilent scanner and images were quantified using the Feature Extraction Software v. 9.3 (Agilent).

Data type: Epigenomics

Sample scope: Multiisolate

Relevance: Medical

Release date: 2009-08-29

Last updated: 2009-08-27