Ludwig Institute/UC San Diego ChIP-chip tracks   (All Pilot ENCODE Chromatin Immunoprecipitation tracks)

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LI ChIP Various  Ludwig Institute/UCSD ChIP-chip: Pol2 8WG16, TAF1, H3ac, H3K4me2, H3K27me3 antibodies  Source data version: ENCODE June 2005 Freeze
LI gIF ChIP  Ludwig Institute/UCSD ChIP-chip - Gamma Interferon Experiments  Source data version: ENCODE June 2005 Freeze
LI Ng gIF ChIP  Ludwig Institute/UCSD ChIP-chip NimbleGen - Gamma Interferon Experiments  Source data version: ENCODE June & Oct 2005 Freezes


This super-track combines related tracks of ChIP-chip data generated by the Ludwig Institute/UCSD ENCODE group. ChIP-chip, also known as genome-wide location analysis, is a technique for isolation and identification of DNA sequences bound by specific proteins in cells, including histones. Histone methylation and acetylation serves as a stable genomic imprint that regulates gene expression and other epigenetic phenomena. These histones are found in transcriptionally active domains called euchromatin.

These tracks contain ChIP-chip data for transcription initiation complex (such as Pol2 and TAF1) and H3, H4 histones in multiple cell lines, including HeLa (cervical carcinoma), IMR90 (human fibroblast), and HCT116 (colon epithelial carcinoma), with some experiments including interferon-gamma induction.


The data for this track were generated at the Ren Lab, Ludwig Institute for Cancer Research at UC San Diego.


Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B. Direct isolation and identification of promoters in the human genome. Genome Res. 2005 Jun;15(6):830-9.

Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8164-9.

Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E et al. Genome-wide location and function of DNA-associated proteins. Science. 2000 Dec 22;290(5500):2306-9.

Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. A high-resolution map of active promoters in the human genome. Nature. 2005 Aug 11;436(7052):876-80.