GSE20673
Genome-wide mapping of H3K4me3 and of PHF8 and ZNF711 binding sites in SH-SY5Y cells
We analyzed the genome wide binding sites for the potential XLMR genes PHF8 and ZNF711 in  the neuroblastoma cell line SH-SY5Y using antibodies specific for PHF8 and ZNF711 and correlated this with binding pattern of H3K4me3.  The total number of peaks detected for PHF8 based on 9.8 million sequence reads, 9.6 million sequence reads for ZNF711 and 9.1 million sequence reads for H3K4me3 after IgG normalization were 17075, 1875 and 19534, respectively. Annotation of the peaks to genes using the hg18 genome database revealed 10039 genes positive for H3K4me3, 7682 were bound by PHF8 and 1103 genes were bound by ZNF711 within +/-1000bp from TSS. As former genome wide analysis of H3K4me3 revealed is this histone mark preferentially associated with transcription start sites. The analysis revealed that 82% of H3K4me3 positive genes are also positive for PHF8. In general, PHF8 either co-localizes or partly overlaps with regions positive for H3K4me3 and covers the putative TSS of the target genes. Overall design: Examination of two different proteins and one histone modification in a human neuroblastoma cell line