Cindy Boer

Epigenomics in bone and cartilage disease | 47 1.2 Table 3: Publicly Available Epigenetics Data on Bone and Cartilage Cells Project Cell Type Source Experiment Data Combined data Ref. ENCODE Chondrocyte Primary cells Knee articular chondrocyte RNA‐seq Small RNA expres- sion Total RNA expression [114] Osteoblast Primary cells RNA‐seq RNA‐mi- croarray CAGE RRBS DNase‐seq ChIP‐Seq Small RNA expres- sion Total RNA expression Tran- scriptional start sites Methylation DNA accessibility Histone marks: H2AFZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3, H3K79me2, H3K9me3, H4K20me1 DNA binding proteins: CTCF, EP300 Full reference epigenome by ROADMAP: E129 [4, 113] ROADMAP Chondrocyte Cultured cells Mesenchy mal stem cell derived ChIP‐Seq CAGE Transcriptional start sites Histone marks: H3K27ac, H#K27me3, H3K36me3, H3K4me1, H3K4me3, H3K- 9ac, H3K9me3 Full reference epigenome by ROADMAP: E049 FANTOM5: active enhancers [4, 113, 182] ENCODE=encyclopedia of DNA elements; ROADMAP=Roadmap Epigenomics Mapping Consortium; RNA‐seq=RNA sequencing; CAGE=cap analysis gene ex- pression; RRBS=reduced representation bisulfite sequencing; DNase‐seq=DNase‐I hypersensitive sites sequencing; ChIP‐seq=chromatin immunoprecipitation sequencing.