This repository contains a description of the computational methods associated to the manuscript (include link).
Details about the "fundamental" analyses are given in the following sections:
- 5fC pull down
- MNase-seq
- RNA-seq
- Reconstitution experiments
- Histone mark and CpG island datasets used
- Polymerase stop assays
- gDNA with only C, 5mC, 5hmC or 5fC
- Chip-seq H3 histone crosslinked to 5fC
- GRO-seq analysis on mESC
The following analysis are derived from data generated in the sections above:
- 5fC sites in heart/brain for WT and TDG-KO
- 5fC-related gene expression in mouse embrio heart and brain
- Nucleosome enrichment in H3K27ac, H3K4me1 and CpG island, with or without 5fC.
- Generating random control sequences with the same CG enrichment profile as the reference.
- Plot nucleosome occupancy 5fC vs non5fC in vitro with the same CG enrichment (notebook)