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The Agilent Gene Expression Platform
LINC-ing To The Future with Increased Density
Gene expression continues to be a core component of systems biology studies. As the
perspective of systems biology continues to change, it is imperative that the platforms involved
in gene expression continue to evolve. With that concept in mind, Agilent Technologies has
launched the new SurePrint G3 Gene Expression Microarray platform. The G3 GE platform has
undergone a redesign based on updated databases to ensure comprehensive coverage of
current content. In addition, the G3 GE platform has increased density to allow for expanded
content. One of the most exciting ways this expanded content is being utilized is with the
addition of non-coding RNAs, specifically lincRNAs, now making it possible to perform two
experiments from a single data set. Come see how this new design with updated and expanded
content can take your research into the future.
David Weiss
Field Application Scientist
Agilent Technologies
November 18, 2010
Systems BiologyKeys To A Successful Experiment
• Flexibility
• Sensitivity
• Dynamic Range
• Data Quality and Reproducibility
Agilent Confidential
For research use only. Not for use in
diagnostic procedures
Agilent Delivers With
A Complete Workflow!
FlexibilityCatalog and Custom Arrays through eArray• Wide range of catalog microarrays available
– Human, Mouse, Rat, Bovine, C.elegans, Canine, Chicken, Drosophila, Horse, Mosquito, Porcine,
Rabbit, Rhesus Macaque, Salmon, Sheep, Xenopus, Zebrafish
– Arabidopsis, Barley, Brassica, Cotton, Maize, Medicago, Rice, Tobacco, Tomato, Wheat
– E. coli, Magnaporthe, Yeast
• Unlimited custom microarray options in eArray
– Choose Agilent-optimized probes, upload your own sequences, or design probes
– Search and download Agilent catalog microarray content and include in your designs
ORANGE: Catalog arrays available in SurePrint G3 8x60K format
FlexibilityAgilent Microarray Manufacturing
AGILENT
- Industrial
manufacturing facility –
Class 10,000 clean-
room
- Ability to easily scale
production capacity –
NO delays
Nature Biotech. 19(4), 342-347 (2001).
FlexibilityG3 Format Features
• Comprehensive coverage
– Updated content
– Inclusion of non-coding RNAs, for the first time!
• Higher throughput for whole-genome studies
• Lower RNA input requirement (down to 10 ng)
• Increased affordability
• Increased density
– Combine species on a single array; for example, human + pathogens
– Target exons or splice junctions
– Replicate probes
Agilent Confidential
For research use only. Not for use in
diagnostic procedures
SurePrint G3 Arrays
FlexibilityMultiple Gene Expression Microarray Configurations
SurePrint HD Arrays
1x
2x
4x
8x
65 µm features
Compatible with:
Agilent B or C Scanner
30 µm features
Compatible with:
Agilent C Scanner
For research use only. Not for use in
diagnostic procedures
60K15K
44K180K44K44K
44K400K44K105K
44K 1M44K 244K
SensitivityAccurate Representation of Low & High Abundance Transcripts
• All Agilent microarrays include probes for spike-in controls, which indicate labeling
and hybridization success
• Agilent spike-ins demonstrate
• Sensitive detection on the order of 1 in 6.9 million transcripts
• Detection across a dynamic range spanning 5 orders of magnitude
Dynamic RangeWide Dynamic Range for Sensitivity to Low Expressors
• Agilent gene expression data provides the expected normal distribution of signals, with few
probes in the noise
• Competing platforms suffer from compressed signals without a normal distribution
Dynamic RangeAdvantages
• 5 log Dynamic
Range allow detect
both high and low
abundant
transcripts
MCF-7
GO analysis for each Expression range
Metabolism
Biosynthesis
Regulation of transcription
Signal transduction
Data Quality & ReproducibilityComparison of Tumor & Normal Samples
• Various tissue samples and types provide similar levels of high
reproducibility using SurePrint G3 Gene Expression Microarrays
• Reproducibility translates in the ability to confidently identify genes of
differential expression
For research use only. Not for use in
diagnostic procedures
~5 o
rders
of m
agnitude
AdenocarcinomaNormal Colon
Replicate #2
Replicate #3
Rep
lic
ate
#1
Re
pli
ca
te #
2
Replicate #2
Rep
lic
ate
#
1
Replicate #3
Rep
lic
ate
#
2
Data Quality & ReproducibilityHigh Concordance and Correlation to TaqMan Data
• As compared with other microarrays providers, Agilent array gene expression signals span
a wider dynamic range
• With wide dynamic range, Agilent gene expression data reflect real gene expression levels
TaqMan Log Ratio
Mic
roa
rray L
og
Ra
tio
10 ng Input: n = 686, r = 0.93, m = 0.86
50 ng Input: n = 704, r = 0.94, m = 0.90
Agilent Array Correlation to Taqman
For research use only. Not for use in
diagnostic procedures
Data Quality & ReproducibilityIntra-Array Reproducibility
• High intra-array reproducibility indicated by low % coefficient of variance
between replicate probes on individual arrays
• SurePrint G3 arrays provide data you can trust
% C
V P
roce
sse
d S
ign
al
1x1M 2x400K 4x180K 8x60K
6
4
10
8
MAQC A
MAQC B
For research use only. Not for use in
diagnostic procedures
Data Quality & ReproducibilityInter-Array Reproducibility• High inter-array reproducibility indicated by low % coefficient of variance
between replicate probes on individual arrays
• SurePrint G3 arrays provide data you can trust
# G
en
es
De
tec
ted
CV
(%
)
For research use only. Not for use in
diagnostic procedures
Data Quality & ReproducibilitySurePrint G3 Microarrays and RNA-Seq: a Comparison
• Strong correlation of log ratios are observed
between microarray and RNA-Seq for
samples MAQC A and B
• Microarrays are faster, easier, more
affordable, and require little RNA input
Scatter Plot
B
M = 1.120
R = 0.840
N = 15516
RN
A-S
eq,
1 µ
g
8x60K, 25 ng, 1-color
Array and RNA-Seq
Log2 Ratios (B/A)
Agilent G3
+LIQARNA-Seq
Starting Material 10 ng 1 µg
Total Sample Prep 6.5 hr 11.5 hr
Hands-on Sample
Prep1.5 hr 3.75 hr
Sample to Data 1.5 days ~ 1 week
Analysis Simple Challenging
Price per sample $$ $$$
For research use only. Not for use in
diagnostic procedures
A Complete Solution for Gene Expression• RNA purification
• RNA quality assessment
• Catalog arrays for 30 species
• Unlimited custom array
options
• Simple assay with low RNA
input requirement
• Quality controls
• Biological interpretation
• qRT-PCR validation
Array Selection & Creation
Sample Labeling
Genome-wide & Custom ArraysHyb & Wash
Scanning and Feature Extraction
Data Analysis
Sample Prep and QA
qRT-PCR Validation
SurePrint G3
Exon Arrays
GeneSpring 11.5
Gene Expression Equipment List
Agilent Confidential
For research use only. Not for use in
diagnostic procedures
Part Number Description Format
# Arrays per
Slide Qty/Kit Part Number Description Qty/Kit
G4851A SurePrint G3 Human GE 8x60K Kit 8x60K 8 3 5188-5279 Two-color RNA Spike-in Kit
G4852A SurePrint G3 Mouse GE 8x60K Kit 8x60K 8 3 5188-5282 One-color RNA Spike-in Kit
G4853A SurePrint G3 Rat GE 8x60K Kit 8x60K 8 3 5190-2305
Low Input Quick Amp Labeling
Kit, One-Color 24 rxns
G4102A SurePrint G3 Custom GE 8x60K 8x60K 8 1 5190-2306
Low Input Quick Amp Labeling
Kit, Two-Color 48 rxns
G4862A SurePrint G3 Custom GE 4x180K 4x180K 4 1 5188-5242
Gene Expression Hybridization
Kit
G4861A SurePrint G3 Custom GE 2x400K 2x400K 2 1 5185-5974 25X Fragmentation Buffer 10mls
G4860A SurePrint G3 Custom GE 1x1M 1x1M 1 1 5188-5281
10X Gene Expression Blocking
Agent, Large Volume
G4845A Human GE 4x44K v2 Microarray Kit 4 x 44K 4 5 5190-0403 2X Hi-RPM Hybridization Buffer 25mls
G4846A Mouse GE 4x44K v2 Microarray Kit 4 x 44K 4 5 5188-5325 Gene Expression Wash Buffer 1 4L
G4131F Whole Rat Genome Microarray Kit 4 x 44K 4 5 5188-5326 Gene Expression Wash Buffer 2 4L
G2514F Custom Microarray GE 4 x 44K 4 1 G2565CA
Agilent High-Resolution
Microarray Scanner Bundle
G4503A Custom Microarray GE 2 x 105K 2 1 G2534A
Hybridization Chamber,
Stainless
G4502A Custom Microarray GE 1 x 244K 1 1 G2534-60003 Backing Slides 5
G2509F Custom Microarray GE 8 x 15K 8 1 G2545A Hybridization Oven
G2530-60029 Hybridization Oven Rotator
G2939AA
2100 electrophoresis
Bioanalyzer (no PC!)
5067-1511 Agilent RNA 6000 Nano Kit 300