UVa DNA Rep Tracks
 
University of Virginia DNA Replication Timing and Origins tracks   (All Pilot ENCODE Chromatin Structure tracks)

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UVa DNA Rep  University of Virginia Temporal Profiling of DNA Replication  Source data version: ENCODE June 2005 Freeze
UVa DNA Rep Seg  University of Virginia DNA Replication Temporal Segmentation  Source data version: ENCODE Oct 2005 Freeze
UVa DNA Rep Ori  University of Virginia DNA Replication Origins  Source data version: ENCODE Oct 2005 Freeze, May 2007 data
UVa DNA Rep TR50  University of Virginia DNA Smoothed Timing at 50% Replication  Source data version: ENCODE Oct 2005 Freeze

Overview

This super-track combines related tracks of DNA replication data from the University of Virginia. DNA replication is carefully coordinated, both across the genome and with respect to development. Earlier replication in S-phase is broadly correlated with gene density and transcriptional activity.

These tracks contain temporal profiling of DNA replication and origin of DNA replication in multiple cell lines, such as HeLa cells (cervix carcinoma). Replication timing was measured by analyzing Brd-U-labeled fractions from synchronized cells on tiling arrays.

Credits

Data generation and analysis for this track were performed by the DNA replication group in the Dutta Lab at the University of Virginia: Neerja Karnani, Christopher Taylor, Hakkyun Kim, Louis Lim, Ankit Malhotra, Gabe Robins and Anindya Dutta.

Neerja Karnani and Christopher Taylor prepared the data for presentation in the UCSC Genome Browser.

References

Giacca M, Pelizon C, Falaschi A. Mapping replication origins by quantifying relative abundance of nascent DNA strands using competitive polymerase chain reaction. Methods. 1997 Nov;13(3):301-12.

Mesner LD, Crawford EL, Hamlin JL. Isolating apparently pure libraries of replication origins from complex genomes. Mol Cell. 2006 Mar 3;21(5):719-26.

Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A. 2005 May 3;102(18):6419-24.