Fig. 2

Gene expression dynamics and chromatin accessibility dynamics during CIP with or without BrdU/IdU. A Schematic diagram of the induction of CiPSCs from MEFs. B Heatmap of RNA-seq for CIP at D8, 14, 20 and 26 with or without BrdU or IdU. C The global chromatin status of closed in MEFs but open in ESCs (CO)/ open in MEFs but closed in ESCs (OC) and permanent open (PO) for CIP at D8,14,20,26 and 40 with or without BrdU or IdU. D Representative fibroblast genes, XEN genes and pluripotency genes peaks from ATAC-seq for CIP at D8, 14, 20 and 26 with or without BrdU or IdU. E The global chromatin status of CO/OC and PO arranged as groups for CIP at D8, 14, 20, 26 and 40 with or without BrdU or IdU. F TF motifs enriched at least twofold for CO/OC loci defined by ATAC-seq peaks with or without BrdU or IdU. TF families are indicated on the right of the heatmap. G Statistical analysis of number of total peaks in CO1-6/OC1-6. H Venn diagrams of OC1-6/CO1-6 peaks between samples with or without BrdU or IdU