Instrument: Illumina Genome Analyzer IIx
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: For Ptf1a and Rbpj E12.5 neural tube mouse embryos placed in Buffer A (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose) on ice. Nuclei were liberated by Dounce homogenization and purified by centrifugation through a sucrose gradient (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.1 mM EDTA, 0.25 mM EGTA, 1.25 M sucrose). Nuclei were then fixed in 1% formaldehyde for 10 minutes at 30°C, and fixation was terminated by adding glycine to a final concentration of 0.125 M. After centrifuging through another sucrose gradient, fixed nuclei were lysed in sonication buffer (1% Triton, 0.1% sodium deoxycholate, 150 mM NaCl, 50 mM Tris, 5 mM EDTA). Chromatin was sheared using a Diagenode Bioruptor for 30 minutes on high power with 30 second on:off cycles. For Ascl1, ChIP E12.5 mouse neural tubes were dissected into PBS then fixed in 1% formaldehyde for 15 min and lysed in 1% SDS, 10 mM EDTA, and 50 mM Tris. Sonication was performed using a Bioruptor (Diagenode) at high power settings for 45 cycles (30 sec on/30 sec off). All libraries were made according to Illumina’s ChIP-seq DNA sample prep protocol