Figure 1

Chromatin immunoprecipitation coupled with Affymetrix high-density tiling arrays (ChIP-on-chip) is a powerful technique for identifying transcription factor binding sites, sites of histone modification, DNA methylation and other regulatory elements. High-density GeneChip® Tiling Arrays offer unrivaled genome coverage, enabling you to detect functional elements that would be missed with other platforms.

Greatest Coverage with the Fewest Number of Arrays

Get the most out of your epigenetics and gene regulation studies. With 6.4 million features per array and 25-mer probes spaced every 35 base pairs (bp) across an entire genome, GeneChip® Tiling Arrays offer complete and unbiased whole-genome coverage on the smallest number of arrays. Whole-genome coverage is available in seven-array sets for human and mouse, and single-array designs for Arabidopsis, Drosophila, Caenorhabditis elegans, Saccharomyces cerevisiae and Schizosaccharomyces pombe—detect more, with fewer arrays. Single-array designs are available for chromosome 21/22, ENCODE regions and human and mouse promoter regions.

Powerful Solutions for Advanced Gene Regulation Analysis

With a detailed protocol, robust reagents, industry-standard arrays and a variety of comprehensive data analysis solutions, the Affymetrix ChIP-on-chip toolbox can help you throughout your experiment—from pre-immunoprecipitation to publication. Preliminary data and visualization of peaks is performed with Tiling Array Software and Integrated Genome Browser, which can be downloaded free of charge. Advanced, downstream data analysis can be performed with several GeneChip-compatible™ or academic software packages.

Featured Products

GeneChip® Tiling Arrays for ChIP-on-chip

GeneChip® Tiling Arrays for ChIP-on-chip enable you to explore and identify functional elements of the genome, including transcription factor binding sites, DNA methylation and histone modification. With 6.4 million features per array and 25-mer probes spaced every 35 base pairs (bp), GeneChip Tiling Arrays offer more content per array than any other platform.

Whole-genome Coverage:

• Human Tiling 2.0R Array Set*
• Mouse Tiling 2.0R Array Set*
• Drosophila 2.0R Array
• Arabidopsis Tiling 1.0R Array
• C. elegans 1.0R Array
• S. pombe Tiling 1.0FR Array
• S. cerevisiae Tiling 1.0R Array

*Single arrays are also available

Promoter and Focused Content:

• Human Promoter 1.0R Array
• Mouse Promoter 1.0R Array
• Chromosome 21/22 2.0R Array
• Encode 2.0R Array

Tiling Array Tools

Tiling Array Software (TAS) and the Integrated Genome Browser (IGB) are available for preliminary data analysis and visualization of peaks. Advanced data analysis can be performed with a variety of GeneChip-compatible™ and academic software packages.

Webinars & Interviews

ChIP Analysis Using Genomatix' ChipInspector: A Biology-driven Approach

Review a conference call symposium and Q&A featuring Martin Seifert, Ph.D., Vice President of Microarray Research, Genomatix.

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Analysis of ChIP-on-chip Data Using Affymetrix Genome Tiling Microarrays

Review a conference call symposium and Q&A featuring X. Shirley Liu, Ph.D., Assistant Professor of Biostatistics, Dana-Farber Cancer Institute, Harvard School of Public Health.

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Demonstration of Partek® GS for ChIP-on-chip Regulation Studies using Affymetrix Tiling Arrays

Review a conference call symposium and Q&A featuring Tom Downey, M.Sc., President and Data Analysis Consultant, Partek.

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The Genpathway/Affymetrix Total Solution for ChIP-on-chip and Methylated DNA IP-on-chip Assays

Review a conference call symposium and Q&A featuring Mary Warren, Ph.D., Chief Scientific Officer, Genpathway.

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ChIP-on-chip: Defining the Estrogen Receptor Cistrome

Review a conference call symposium and Q&A featuring Myles Brown, M.D., Professor of Medicine, Harvard Medical School and Dana-Farber Cancer Institute.

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ChIP-on-chip Theory and Applications

Philipp Kapranov, Ph.D., Staff Scientist, Affymetrix

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Genome-wide Analysis of Epigenetic Modification Yields New Clues to Malignant Glioma Diagnosis and Treatment

The Swedish Medical Center's Anup Madan and MIT's Noam Shomron discuss new insights into the epigenetic regulation of the molecular pathways behind malignant glioma.

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High-resolution Tiling Arrays Used to Map Genome-wide Methylation Patterns in Arabidopsis

The Salk Institute's Joseph Ecker and Lawrence Livermore's Jutta Kollet discuss the first study to map the methylome in Arabidopsis.

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New Bioinformatics Algorithm Predicts Forkhead Protein Plays a Role in Breast Cancer Estrogen Response

Dana-Farber's Shirley Liu and Lawrence Berkeley National Laboratory's David Nix weigh in on improved algorithms for ChIP-on-chip experiments.

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Novel Combination of Chromatin Modifications Governs Embryonic Stem Cell Maintenance

Harvard Medical School's Bradley Bernstein talks with UT Southwestern's Ryan Weil about how bivalent methylation may control the timing of cell division and differentiation in stem cells.

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Thousands of Previously Unknown Transcription Factor Binding Sites Mapped Using Tiling Microarrays

Harvard's Kevin Struhl and Dana-Farber's Myles Brown discuss ChIP-on-chip as an unbiased method for transcription factor binding site identification.

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Genome-wide Mapping of Estrogen Receptor Binding Sites Workflow

Learn how researchers at the Dana-Farber Cancer Institute and Harvard Medical School, led by Drs. Myles Brown and Shirley Liu, have mapped thousands of estrogen receptor (ER) binding sites in breast cancer cells using ChIP-on-chip.

Affymetrix and Genpathway Collaborate to Provide ChIP-on-chip and Methylated DNA Assays and Services

Read the interview with Marry Warren, Chief Scientific Officer at Genpathway.

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Publications and References:

"Bibliography of Affymetrix Tiling Publications" for the tiling array publication

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