Agilent Mouse Promoter Arrays 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 mouse gene regulation
on a genome-wide scale.
Features and Benefits at a Glance
Probes provide coverage for ~17,000 of
the best defined mouse transcripts (as
defined by RefSeq) and cover –5.5 KB
upstream to +2.5 KB downstream from
the transcriptional start sites for our
promoter arrays.
Superior Microarray Performance
Proprietary microarray technology using
optimized 60-mer oligonucleotide probes
and a convenient two-color labeling
system delivers 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
Complete access to public databases,
probe sequences, and annotation files
for convenient 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.
Mouse Promoter Arrays
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
5989-4321EN
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 nonspecific noise.
*Probes are designed with criteria including
optimal Tm, unique sequence, and self-structure
prediction.
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Product number
Slides/set
Minimum order
Microarrays/slide
Design ID numbers
Microarray format
Probe length
Probes/Transcript
Probe coverage
Agilent internal quality control probes
Sequence source
Feature size
Starting sample input
DNA required for labeling
Type of labeling
DNA required for hybridization
Hybridization volume
Specifications
Mouse Promoter Set
G4490A
2
5 sets (10 slides)
1
014716, 014717
244K
60 bases
~25 probes
~17,000 of the best defined
mouse transcripts and cover
–5.5 KB upstream to +2.5 KB
downstream from the transcriptional
start sites
~5000
UCSC mm7/NCBI release 35
(August 2005)
65 µm
0.5 x 10
7
–1 x 108cells
2 µg
Random priming using Klenow
with Cyanine 3 and Cyanine 5 nucleotides
5 µg per channel
500 µL
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