Genome-wide nucleosome occupancy profiling by high throughput sequencing, and microarray analysis of RNA abundance

We profiled nucleosome occupancy of different developmental stages in C. elegans. Mononucleosomal DNA was sequenced by Illumina paired-end sequencing. We used embryos, germlineless adults, germ line containing adults, and XO hermaphrodites at L3 larval stage. RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf After MNase digestion of chromatin, we purified mononucleosomal DNA and used Illumina paired-end sequencing. Mapping was done in embryo (strain N2), germlineless adults (strain JK1107), germ line containing adults (strain DH245),and XO hermaphrodites (strain TY2205) at L3 larval stage. For each experimental replicate RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase.