Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos [ChIP-seq]

Chromatin profiling of affinity-purified nuclei of neural stem cells (NSCs) and neurons from the Drosophila embryos, respectively. Cell type-specific nucleosome and histone modification maps were generated from NSCs and neurons nuclei, which isolated from 5–7h-old Sca-Gal4/cyo;UAS-3xFLAG-blrp-mCherry-RanGap and 12–14h-old Elav-Gal4;UAS-3xFLAG-blrp-mCherry-RanGap D. melanogaster embryos using the method INTACT (Steinner et al., 2012). We determinated nucleosome occupancy in these nuclei by micrococcal nuclease sequencing (MNase-Seq). We also performed ChIP-Seq (chromatin immunoprecipitation and sequencing) for five histone modifications (H3K4me3, H3K4me1,H3K9ac, H3K27ac, and H3K27me3). Sequencing was performed on Illumina HiSeq 2000 using signle end protocol.