This multilayer omics dataset involves the information on DNA replication timing, promoter CpG classification and gene expression. It consists of digitised replication timing, promoter CpG status and expression levels of 17,292 genes in a variety of samples.
load(url("http://dnet.r-forge.r-project.org/data/Datasets/Hiratani_TableS1.RData"))
RT: a replication timing matrix of 17,292 genes X 22 samples. These 22 samples come from 22 cell lines during early mouse embryogenesis, and they can be categorised into: 1) pluripotent cells, including ESCs (ESC_46C, ESC_D3 and ESC_TT2) and iPSCs (iPSC, iPSC_1D4 and iPSC_2D4); 2) partially-reprogrammed iPSCs (piPSC_1A2, piPSC_1B3 and piPSC_V3); 3) early epiblast (EPL and EMB3_D3); 4) late epiblast (EpiSC5 and EpiSC7); 5) Ectoderm (EBM6_D3, EBM9_D3, NPC_46C and NPC_TT2); 6) Mesoderm and Endoderm; and 7) late Mesoderm (Myoblast, MEF_female and MEF_male).
CpG: a matrix of 17,292 genes X 1 containing gene additional information on promoter CpG classification, with '1' for HCP (high CpG density promoters), '-1' for LCP (low CpG density promoters), '0' for ICP (intermediate CpG density promoters), and 'NA' for unclassified.
EX: an expression matrix of 17,292 genes X 8 samples, and samples include pluripotent cells (ESC_D3); early epiblast (EMB3_D3); late epiblast (EpiSC7); Ectoderm (EBM6_D3 and EBM9_D3); Mesoderm and Endoderm.
Mikkelsen et al. (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448:553-560.
Hiratani et al. (2010). Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Research, 20:155-169.
load(url("http://dnet.r-forge.r-project.org/RData/1.0.7/Hiratani_TableS1.RData")) ls() # you should see three variables: 'RT', 'CpG' and 'EX'[1] "CpG" "EX" "RT"