File S1 - Dynamic Nucleosome Organization at hox Promoters during Zebrafish Embryogenesis

File with Figures S1 and S2. Figure S1 Comparison of biological replicates used for calculation of nucleosome densities. Data from two biological replicates were plotted against each other for untreated embryos at 2 hpf (A), 4 hpf (B), 6 hpf (C), 9 hpf (D), as well as for RA-treated embryos at 2 hpf (E), 4 hpf (F), 6 hpf (G), 9 hpf (H) and for DEAB-treated embryos at 9 hpf (I). R2 values are indicated in the top right quadrant of each panel. Figure S2 Representative MNase digestion. Cross-linked genomic DNA from 4 hpf embryo was left untreated (lane 2) or treated for 10 minutes at 37°C with serially diluted concentrations of micrococcal nuclease (MNase) increasing from 0.5 units/ml −8 units/ml (lanes 3–6) and separated by agarose gel electrophoresis. Lanes 1 and 7 contain size ladders. (PDF)

包含补充图S1与S2的文件。补充图S1：核小体密度计算所用生物学重复样本的比对分析。将未处理的受精后2小时（2 hpf, hours post fertilization）胚胎（A）、4 hpf胚胎（B）、6 hpf胚胎（C）、9 hpf胚胎（D）的两组生物学重复数据进行交叉绘图；同时分别绘制视黄酸（Retinoic Acid, RA）处理的2 hpf胚胎（E）、4 hpf胚胎（F）、6 hpf胚胎（G）、9 hpf胚胎（H），以及4-二乙氨基苯甲醛（4-(Diethylamino)benzaldehyde, DEAB）处理的9 hpf胚胎（I）的重复数据比对图。每个子图的右上角均标注了决定系数R²值。补充图S2：代表性微球菌核酸酶（Micrococcal Nuclease, MNase）消化实验结果。提取4 hpf胚胎的交联基因组DNA，设置未酶处理对照组（泳道2），另取样本在37℃下用梯度稀释的微球菌核酸酶（MNase）处理10分钟，酶浓度依次从0.5单位/毫升升至8单位/毫升（泳道3至6），随后通过琼脂糖凝胶电泳分离。泳道1与泳道7为DNA分子量标准。（PDF）