Affy ChIP Tracks
 
Affymetrix ChIP-chip tracks   (All Pilot ENCODE Chromatin Immunoprecipitation tracks)

Display mode:   

 All
Affy pVal  Affymetrix ChIP-chip (retinoic acid-treated HL-60 cells) P-Value  Source data version: ENCODE June 2005 Freeze
Affy Sites  Affymetrix ChIP-chip (retinoic acid-treated HL-60 cells) Sites  Source data version: ENCODE June 2005 Freeze
Affy Strict pVal  Affymetrix ChIP-chip (HL-60 and ME-180 cells) Strict P-Value  Source data version: ENCODE Oct 2005 Freeze
Affy Strict Sig  Affymetrix ChIP-chip (HL-60 and ME-180 cells) Strict Signal  Source data version: ENCODE Oct 2005 Freeze
Affy Strict Sites  Affymetrix ChIP-chip (HL-60 and ME-180 cells) Strict Sites  Source data version: ENCODE Oct 2005 Freeze

Overview

This super-track combines related tracks of ChIP-chip data generated by the Affymetrix/Harvard ENCODE collaboration. 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.

These tracks contain ChIP-chip data of multiple transcription factors, RNA polymerase II and histones, in multiple cell lines, including HL-60 (leukemia) and ME-180 (cervical carcinoma), and at different time points after drug cell treatment. Binding was assayed on Affymetrix ENCODE tiling arrays. Data are displayed as signals, median p-values, "strict" p-values and sites.

Credits

These data were generated and analyzed by collaboration of the Tom Gingeras group at Affymetrix and the Kevin Struhl lab at Harvard Medical School.

References

Please see the Affymetrix Transcriptome site for a project overview and additional references to Affymetrix tiling array publications.

Bolstad BM, Irizarry RA, Astrand M, and Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003 Jan 22;19(2):185-93.

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004 Feb 20;116(4):499-509.