Exploring the relationship between 5fC and nucleosomal organization in tissues obtained from mouse embryos E11.5 and synthetic DNA

To investigate the impact of 5fC on nucleosome organization, samples from hindbrain and heart tissues of mouse embryos at 11.5 days of development were processed: - To extract genomic DNA, combine it with HeLa nucleosomes and buffer followed by sequencing to provide a map of in vitro reconstituted mononucleosomes. - Tissues were incubated with MNase digestion buffers followed by sequencing to produce in vivo nucleosome maps (MNase-seq) - To extract RNA to investigate transcript levels (RNA-seq) To locate positions of covalent interactions between 5fC and histone lysines we performed polymerase stop assays using a single primer extension followed by sequencing to identify stalled sites. 5fC sites were previously obtained in E-GEOD-77447 (pubmed:27356509) Histone marks were previously identified in E-GEOD-82454, E-GEOD-82888 and E-GEOD-82484