DNA replication Track Settings
 
DNA replication   (All R-loopBase Data tracks)

Display mode:       Reset to defaults   
Type of graph: Graph configuration help
Track height: pixels (range: 10 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 127)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Select subtracks by cell line and technology: (help)
 All Cell Line MEF  mESC  Activated-primary-B-cells 
Technology
OK-seq 
Repliseq 
List subtracks: only selected/visible    all    ()
  Cell Line↓1 Technology↓2   Track Name↓3  
hide
 Configure 		 Activated-primary-B-cells  OK-seq  bigwig_7_Activated-primary-B-cells_OK-seq_rep2   Schema 
hide
 Configure 		 Activated-primary-B-cells  OK-seq  bigwig_8_Activated-primary-B-cells_OK-seq_rep3   Schema 
hide
 Configure 		 Activated-primary-B-cells  OK-seq  bigwig_6_Activated-primary-B-cells_OK-seq_rep1   Schema 
hide
 Configure 		 MEF  Repliseq  bigwig_Repliseq_MEF_S4   Schema 
hide
 Configure 		 MEF  Repliseq  bigwig_Repliseq_MEF_S3   Schema 
hide
 Configure 		 MEF  Repliseq  bigwig_Repliseq_MEF_S2   Schema 
hide
 Configure 		 MEF  Repliseq  bigwig_Repliseq_MEF_S1   Schema 
hide
 Configure 		 MEF  Repliseq  bigwig_Repliseq_MEF_G1   Schema 
hide
 Configure 		 mESC  OK-seq  bigwig_9_mESC_OK-seq_rep1   Schema 
hide
 Configure 		 mESC  OK-seq  bigwig_10_mESC_OK-seq_rep1   Schema 
hide
 Configure 		 mESC  Repliseq  bigwig_Repliseq_mESC_S4   Schema 
hide
 Configure 		 mESC  Repliseq  bigwig_Repliseq_mESC_S3   Schema 
hide
 Configure 		 mESC  Repliseq  bigwig_Repliseq_mESC_S2   Schema 
hide
 Configure 		 mESC  Repliseq  bigwig_Repliseq_mESC_S1   Schema 
hide
 Configure 		 mESC  Repliseq  bigwig_Repliseq_mESC_G1   Schema 
    

Description

This track integrates genome-wide datasets related to DNA replication, including Repli-seq and OK-seq. Repli-seq measures replication timing across the genome by profiling newly synthesized DNA from cells isolated at different stages of S phase, whereas OK-seq maps replication fork directionality based on the distribution of Okazaki fragments. Together, these datasets provide complementary information on replication timing, fork progression, and the organization of DNA replication across the genome. Genomic coordinates were lifted from the mm10 assembly to mm39 using LiftOver.

Reference

Rodriguez-Carballo E, Dionellis VS, Ntallis SG, et al, OCT4 enhances the firing efficiency of late DNA replication origins in mouse embryonic stem cells. Nat Commun. 2026 Jan 15;17(1):1686. PMID: 41540072

Tubbs A, Sridharan S, van Wietmarschen N, et al, Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse. Cell. 2018 Aug 23;174(5):1127-1142.e19. PMID: 30078706

Li Z, Hua X, Serra-Cardona A, et al, DNA polymerase a interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands. Sci Adv. 2020 Aug;6(35):eabb5820. PMID: 32923642