Agilent Human ENCODE User Manual

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GENOMICS

INFORMATICS PROTEOMICS METABOLOMICS

Agilent's novel and powerful method of location analysis of DNA binding

proteins pairs chromatin immunoprecipitation (ChIP) with Agilent DNA

microarrays to allow the construction of comprehensive DNA-protein binding

profiles. This oligonucleotide microarray enables you to use ChIP-on-chip

technology to gain broad insight into the mechanisms of human gene

regulation by studying the ENCODE regions on a genome-wide scale.

Features and Benefits at a Glance

Comprehensive and Genome-Wide

153,000 probes cover chromosomes
1–22 for the ENCODE regions.

Superior Microarray Performance

Proprietary microarray technology using
optimized 60-mer oligonucleotide probes
and a convenient two-color labeling
system deliver higher sensitivity,
accuracy, and greater reproducibility
than one-color systems. These unique
features allow sensitive measurements
of weak- and infrequent-binding events,
as well as direct comparisons of
samples on the same microarray.

Reliable Binding Data

Powerful algorithms employ
neighborhood probe voting with multiple
probes to generate reliable data with
greater true-binding events and fewer
false positives.

Agilent SurePrint Technology

Printed using Agilent's SurePrint
technology that features a flexible,
industrial-scale inkjet printing process
that synthesizes oligonucleotide probes

in situ onto 1" x 3" slides. Our
technology provides a means to
consistent, reliable, and affordable
microarray products.

Access to Probe Sequence and
Annotation

Offers convenient access to public
databases and easy extraction of
biological information.

Compatible with Easy-to-Use Data
Analysis Software

ChIP Analytics software combines
annotated, algorithmic array data
processing with an easily manipulated
text file output and high-speed
statistical modeling functions.

Human ENCODE

Agilent ChIP-on-Chip Set

Product Note

Product Note

GENOMICS

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Research use only. Information, descriptions,
and specifications in this publication are subject
to change without notice.

Agilent Technologies shall not be liable for errors
contained herein or for incidental or consequential
damages in connection with the furnishing,
performance or use of this material.

© Agilent Technologies, Inc. 2006

Printed in the U.S.A. August 31, 2006

5989-4324EN

The Agilent Probe Advantage

Unlike other companies, Agilent
provides optimized and validated probe
design that delivers the high signal-to­noise ratios that are essential for the
success of ChIP-on-chip experiments.
We carefully design our probes using
stringent criteria.*

• 60-mer oligonucleotide probes provide
robust hybridization—critical for the
sensitivity and specificity that
ChIP-on-chip demands.

• Average probe spacing parameters
have been specifically optimized for
the ChIP method as compared to other
microarray applications.

• Repeat regions are masked to
significantly reduce non-specific noise.

*Probes are designed with criteria including
optimal Tm, unique sequence, and self-structure
prediction.

Specifications

Product number G4495A

Microarrays/slide 1

Slides/set 1

Design ID numbers 014792

Microarray format 244K

Probe length 60 bases

Probe Coverage Slide 1 Chromosomes 1–22 (~153,000 probes)

Agilent internal quality control probes ~5000

Sequence source Human-ENCODE

Feature size 65 µm

Starting sample input 0.5 x 10

7

–1 x 108cells

DNA required for labeling 2 µg

Type of labeling Random priming using Klenow with

Cyanine-3 and -5 nucleotides

DNA required for hybridization 5 µg per channel

Hybridization volume 500 µL