Gene Expression

NimbleGen Gene Expression Microarrays and Services
High-density arrays for sensitive and accurate
genome-wide gene expression profiling
www.nimblegen.com

Roche NimbleGen offers a comprehensive catalog of gene expression arrays for
whole-genome expression profiling. With the unique combination of long
oligonucleotide probes, flexible array content, and high probe density (up to
385,000 probes per array), NimbleGen Gene Expression arrays enable easy-to-use
and cost-effective analysis of eukaryotic and prokaryotic genomes. Built on the
ultra-high density HD2 platform, the 12x135K array format combines a
multiplex option with high probe density for high-throughput projects.
_________________________ Advantages ______________________________________________________3
_________________________ Protocol _________________________________________________________4
_________________________ Performance Data ______________________________________________5-7
_________________________ Formats and Design Specifications ________________________________8
_________________________ Access Options __________________________________________________9
_________________________ Applications and References _____________________________________10
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Advantages of NimbleGen Gene Expression Microarrays
High-density arrays for high-throughput analysis
More Probes per Transcript
The ultra-high density of NimbleGen DNA
microarrays allows every gene to be represented by
multiple, unique probes on a single array. The signal
averaging of multiple probes provides improved
statistical confidence, reducing the impact of
inconsistent probe behavior and improving the signal
accuracy compared to platforms that offer fewer
probes per gene.
Long Oligos Enhance Accuracy
Roche NimbleGen has the ability to synthesize highdensity
arrays of long oligos. For gene expression
analysis, long oligos (45 - 60mer) provide excellent
signal-to-noise ratio, sensitivity, specificity, and
discrimination, particularly in complex eukaryotic
genomes. Long probes eliminate the need for
mismatch probes, effectively doubling array capacity.
Multiplex Options: Cost-Effective,
High-throughput Analysis
Roche NimbleGen multiplex arrays enable you to
analyze multiple samples in parallel. We offer a 4x72K
format with 72,000 probes per array and a 12x135K
format with 135,000 probes per array. Hybridize four
or 12 samples or run replicate samples on a single
slide and average the data for increased statistical
confidence.
Up-to-date Microarray Design
Roche NimbleGen’s digital microarray manufacturing
process is fast and flexible, allowing you rapid access to
any sequenced genome on an array. All catalog designs
are built from the latest published genomes to ensure
your experiment is current.
High-interarray Reproducibility
NimbleGen arrays are manufactured to exacting
standards and undergo rigorous quality control to
ensure superior interarrray reproducibility. In replicate
hybridization experiments, interarray r 2 values
routinely exceed 0.98.
Flexible Access Options to Best Suit
Your Needs
Roche NimbleGen offers options for both full service
analysis or array delivery for hybridization in your own
lab. Choose to send your RNA or cDNA samples to us
for processing in our full-service laboratory or
hybridize your samples and analyze the data in your lab
using our protocols and reagents.
What users are saying about NimbleGen
Gene Expression 12x135K Arrays:
“Use of the NimbleGen 12x135K gene expression
microarray is advantageous and more accurate than
other platforms because it allows you to run replicates
within the same array that validate analysis within
the same experiment. Also, conducting the array
hybridization is relatively straightforward, and
analysis of the results is user-friendly and does not
require highly specialized informatics skills.”
Licia Selleri, MD, PhD, Associate Professor
Departments of Cell and Developmental Biology
Cornell University Medical School, New York
Advantages
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NimbleGen Gene Expression Protocol
Four easy steps from RNA to differentially expressed genes
A
B
NimbleGen Gene Expression arrays are provided with
fully supported, validated protocols – from sample
preparation through data analysis.
Protocol
1 1
⊳ Figure 1: Gene Expression Analysis Protocol
Contact Roche Microarray Technical Support for complete protocol details.
1. cDNA Synthesis: Eukaryotic (A) or prokaryotic mRNA (B) is converted
via oligo-dT or random priming, respectively, to double-stranded cDNA.
2. cDNA Labeling: The cDNA is labeled with Cy3 dye.
3. Hybridization: Labeled cDNA is hybridized to a NimbleGen Gene
Expression array.
4. Data Analysis: Data are extracted using NimbleScan software and
analyzed for differentially expressed genes.
2
3
4
1 2 3 4 5 6
Hierarchical
Clustering
Universal Human
Reference RNA
Human Brain
Reference RNA
Low Expression High
4 |
Figure 2: Sensitive and Reproducible Detection of Gene
Expression Levels. Two human RNA samples used in the
Microarray Quality Consortium 1 project were analyzed on the
NimbleGen Human Gene Expression 385K array. Genes exhibiting
an 8-fold or higher change between Universal Human Reference
RNA (lanes 1 - 3) and Human Brain Reference RNA (lanes 4 – 6)
were analyzed by hierarchical clustering analysis (far left column)
and plotted as a heat map using the ArrayStar ® software
(DNASTAR, Inc). Orange bars indicate high expression values
while purple bars indicate low expression values.

NimbleGen Gene Expression Performance Data
Accurate, sensitive, and reproducible gene expression profiling
The high quality of NimbleGen Gene Expression
microarrays was proven using the MAQC reference
samples (Universal Human Reference RNA [Stratagene]
and Human Brain Reference RNA [Ambion] 1 ) on highdensity
NimbleGen Human Gene Expression 385K,
4x72K, and 12x135K arrays.
The accuracy of NimbleGen microarray data was
assessed by comparing the fold change values from the
microarrays to the values obtained by COBAS ®
TaqMan ® quantitative PCR assays 1
(Figure 3). Each
point on the scatter plot represents the fold change level
of a gene; a total of 961 genes detected in both the
TaqMan ® assay and NimbleGen array were included in
the analysis. NimbleGen single and multiplex arrays
demonstrate high concordance with TaqMan ® results
and were consistent in correlation with results from
other commercial microarray platforms (Table 1).
Figure 3: Accuracy. The ratio of brain to universal
expression values (log 2
) from NimbleGen Human
Gene Expression 12x135K microarrays were
compared to TaqMan ® data obtained from the MAQC
report. Results show a high concordance (r = 0.92) in
gene expression levels between NimbleGen
microarray and TaqMan ® data.
Performance
Data
Array Correlation with COBAS ® TaqMan ®
NimbleGen 12x135K 0.92
NimbleGen 4x72K 0.92
NimbleGen 385K 0.91
Affymetrix 0.92*
Applied Biosystems 0.85*
Agilent 0.91*
Illumina 0.91*
⊳
Table 1: High-Quality Data Obtained with
NimbleGen Gene Expression Arrays. Log 2
-ratios of
brain RNA to universal RNA gene expression levels
from microarrays from the indicated sources were
compared to the same ratio from TaqMan ® analysis.
*Mean for three test sites, as published by the MAQC Consortium 1 .
1
Nat. Biotechnol. 2006; 24(9: 1151-1161)
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NimbleGen Gene Expression 12x135K Performance Data
Cost-effective, high-throughput whole-genome gene expression profiling
NimbleGen 12x135K microarrays for gene expression
analysis enable you to conveniently and simultaneously
hybridize 12 samples on each slide. These multiplex
arrays offer a cost-effective approach to gene expression
analysis, without compromising information content or
data quality. As with our 385K and 4x72K arrays,
12x135K arrays are available in a broad range of wholegenome
catalog designs or custom design arrays tailored
to your specific experimental goals.
Performance
Data
Advantages
Accurately analyze 12 samples simultaneously on a
single slide.
Achieve high specificity, sensitivity, and reproducibility
with 60mer oligonucleotide probes.
Utilize 135,000 features on each array to include
multiple probes per target:
• Complete coverage of a transcriptome
• Increased accuracy with multiple probes per target
Take advantage of catalog designs based on the most
current whole-genome builds for a variety of
organisms.
Customize array content for any available, annotated
genome.
Figure 5: Reproducibility. Six technical replicates of human brain
RNA were hybridized to NimbleGen Human Gene Expression
12x135K microarrays. High interarray correlations (mean r 2 = 0.99)
are shown in the lower-left panels, and pairwise scatter plots of
gene expression values (log 2
) are shown in the upper-right panels.
Figure 4: Sensitivity. Human brain and universal RNA were
analyzed on NimbleGen Human Gene Expression 12x135K
microarrays (4 technical replicates per sample). High sensitivity
is demonstrated by the wide dynamic range (log 2
of 4 - 16) of
gene expression values on each array.
6 10 14 6 10 14 6 10 14
A01
0.986
6 10 14 6 10 14 6 10 14
A02
0.989 0.988
A03
0.991 0.985 0.987
A04
0.992 0.986 0.987 0.992
A05
0.990 0.986 0.988 0.990 0.992
6 10 14 6 10 14 6 10 14
A06
6 10 14 6 10 14 6 10 14
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NimbleGen Gene Expression Prokaryotic Performance Data
Extensive line of microbial multiplex catalog designs
Prokaryotic Gene Expression Analysis
Roche NimbleGen offers high density arrays for
over 200 Class I, II, and III prokaryotic organisms
in 385K and 4x72K array formats. Because each
385K array contains up to 385,000 features, there is
sufficient probe capacity to tailor an existing array
design to address specific research questions.
Consider including:
Relevant plasmids
Probes from intergenic regions
Probes from multiple organisms
Your own custom controls
NimbleGen 4x72K microarrays for prokaryotic
gene expression analysis enable you to conveniently
and simultaneously hybridize four independent
samples on each slide. These multiplex arrays offer
a cost-effective approach to gene expression
analysis. Similar to our 385K prokaryotic arrays,
these arrays are available in a broad range of wholegenome
catalog or custom designs tailored to your
specific experimental goals.
Figure 6: Sensitivity of NimbleGen E. coli Gene
Expression 4x72K Microarrays. The pairwise scatter plot of
gene expression values (log 2
) for wild type and mutant E. coli
RNA correctly identifies 22 transcripts encoded by genes that
are present in the wild type strain but deleted in the mutant
strain (blue box). The number of genes (and as percent of
total genes) differentially expressed at 2-, 4-, or 8-fold are
indicated in the upper left.
Performance
Data
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NimbleGen Gene Expression Format and Design Specifications
Choice of catalog and custom eukaryotic and prokaryotic
designs for processing in your lab or ours
Catalog Designs
Eukaryotic Gene Expression Arrays
Roche NimbleGen offers a broad range of catalog
eukaryotic arrays for the latest genome builds for human
and the model organisms listed below. Eukaryotic arrays
are available in both single (385K) and multiplex (4x72K
and 12x135K) formats, allowing for both genome-wide
probe coverage and high-throughput analysis.
Custom Designs
For organisms not listed in the NimbleGen product catalog,
custom designed arrays are available for any organism with
high-quality sequence and annotation information. Arrays
can also be customized for your focused region or control
genes (such as probes for spike-ins of known transcripts as
positive controls). Provide us with the target sequences, we
will design the probes and synthesize the arrays.
• Human
• Mouse
• Rat
• Zebrafish
• A. thaliana
• C. elegans
• D. melanogaster
• S. cerevisiae
• S. pombe
385K Array
4x72K Array
12x135K Array
Format and
Design
Specifications
Prokaryotic Gene Expression Arrays
Roche NimbleGen offers the most comprehensive set of
prokaryotic gene expression designs in the industry,
covering over two hundred Class I, II, and III organisms,
including B. subtilis, E. coli, S. enterica, and Y. pestis. Our
high-density arrays allow for every gene in a prokaryotic
genome to be represented by up to 20 unique transcriptspecific
probes and 5 replicate probe sets, depending on
the size of the genome, on a single array, thereby
improving statistical confidence in your results.
Alternatively, simultaneously analyze four samples on a
single 4x72K array for increased throughput without
compromising information content or data quality.
Additionally, there is sufficient probe capacity on each
array to tailor an existing design to address specific
research questions, such as including probes from relevant
plasmids, multiple organisms, or your own custom
controls.
Gene Expression Microarray Formats and Specifications
Format 385K 4x72K 12x135K
Total Probes 385,000 4 x 72,000 12 x 135,000
Probe length (bases) Eukaryote: 60 Eukaryote: 60 Eukaryote: 60
Prokaryote: 45 - 60 Prokaryote: 45 - 60 NA †
Probes per target gene* Eukaryote: 6 - 20 Eukaryote: 2 - 7 Eukaryote: 3 - 7
(catalog designs) Prokaryote: 12 - 25 Prokaryote: 6 - 17 NA †
Replicate probe sets* Eukaryote: 1 - 4 Eukaryote: 1 Eukaryote: 1 - 2
(catalog designs) Prokaryote: 3 - 5 Prokaryote: 2 - 3 NA †
Feature size 16µm x 16µm 16µm x 16µm 13µm x 13µm
Array size 17.4mm x 13.0mm 7.8mm x 5.7mm 8.9mm x 6.5mm
Slide size
1” x 3” (25mm x 76mm)
* Depending on genome size
†
Not Available
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NimbleGen Gene Expression Access Options
Gene Expression arrays available for array delivery or full service
Array Delivery Workflow
1. Select a catalog gene expression array design or work
with Roche NimbleGen Bioinformatics team to create a
custom array.
2. Roche NimbleGen manufactures the array and ships it
to your laboratory.
3. Prepare cDNA samples using the Roche NimbleGen
validated protocol, label and hybridize to the array.
4. Scan array and extract data using NimbleScan software.
5. Identify differentially expressed genes using appropriate
software for expression analysis.
Full Service Workflow
1. Select a catalog gene expression array design or work with
the Roche NimbleGen Bioinformatics team to create a
custom array.
2. Prepare RNA or cDNA samples using validated NimbleGen
protocol and ship them to Roche NimbleGen.
3. Roche NimbleGen manufactures the array and performs
hybridization and data analysis.
4. Roche NimbleGen ships the following:
• Array design files
• Raw gene expression data
• RMA-normalized gene expression data
5. Identify differentially expressed genes using appropriate
software for expression analysis.
Delivery
Select a catalog
design or create
a custom design
Roche
NimbleGen
manufactures
array
Roche
NimbleGen
ships array
to customer
Synthesize
and label
cDNA
Hybridize
sample
Wash
array
Scan
array
Analyze
data
Required Instruments & Kits
Required Kits & Accessories
Required Instruments
Required Software
Service
NimbleGen Hybridization System
NimbleGen Hybridization Kit
NimbleGen Sample Tracking
Control Kit (for multiplex arrays)
NimbleGen Wash Buffer Kit
NimbleGen Array Processing
Accessories
Microarray Scanner
NimbleScan
Access
Options
Select a catalog
design or create
a custom design
Ship samples
to Roche
NimbleGen
Roche
NimbleGen
manufactures
array
Synthesize
and label
cDNA
Hybridize
sample
Wash
array
Scan
array
Roche NimbleGen
performs data
analysis and ships
data to customer
Roche NimbleGen
Customer
| 9
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NimbleGen Gene Expression Applications and References
Take advantage of the inherent flexibility, sensitivity, and
discrimination provided by NimbleGen Gene Expression
microarrays for numerous applications
Applications
Differential Expression
Study gene expression related to multiple signal pathways in
tissues and cells.
Identify factors involved in plant tissue differentiation.
Discover regulatory targets for an orphan two-component
signal regulator and virulence factor in Streptococcus
pneumoniae.
Assess differential gene expression of closely related
protozoan parasites.
References
Batista F, et al. “Potential targets of FOXL2, a transcription factor involved in
craniofacial and follicular development, identified by transcriptomics,” Proc.
Natl. Acad. Sci. USA: 104:3330 (2007).
Pischke M, et al. “A Transcriptome-Based Characterization of Habituation in
Plant Tissue Culture,” Plant Physiol.: 140:1255 (2006).
Motegi M, et al. “Assessment of Genes Associated with Streptococcus mutans
Biofilm Morphology,” Appl. Environ. Microbiol.: 72: 6277 (2006)
Ulijasz A, et al. “Regulation of Iron Transport in Streptococcus pneumoniae by
RitR, an Orphan Response Regulator,” J Bacteriol.: 186:8123 (2004).
Study different but closely related protozoan parasites using a
single expression microarray design.
Tiled Expression
Register the non-coding RNAs in human fibroblasts and yeast.
Identify novel transcripts in rice or Populus trichocarpa.
Catalog global gene expression in Homo sapiens, Drosophila
melanogaster, Chlamydomonas reinhardtii, Arabidopsis thaliana,
or rice.
Confirm bioinformatically identified genes using expression
profiling.
Catalog the global gene expression in rice.
Holzer T, et al. “Expression profiling by whole-genome interspecies microarray
hybridization reveals differential gene expression in procyclic promastigotes,
lesion-derived amastigotes, and axenic amastigotes in Leishmania Mexicana,”
Mol. Biochem. Parasitol. 146:198 (2006).
Rinn J, et al. “Functional Demarcation of Active and Silent Chromatin
Domains in Human HOX Loci by Non-coding RNAs,” Cell: 129:1311 (2007).
Samanta M, et al. “Global identification of noncoding RNAs in Saccharomyces
cerevisiae by modulating an essential RNA processing pathway,” Proc. Natl
Acad. Sci. USA: 103:4192 (2006).
Rinaldi C, et al. “Transcript Profiling of Poplar Leaves upon Infection with
Compatible and Incompatible Strains of the Foliar Rust Melampsora laricipopulina,”
Plant Physiol: 144:347 (2007).
Tuskan G, et al. “The genome of black cottonwood, Populus trichocarpa (Torr.
& Gray),” Science: 313:1596 (2006).
Li L, et al. “Genome-wide transcription analyses in rice using tiling
microarrays,” Genome Biol.: 6:R52 (2005).
Allele-Specific Expression
Identify allele-specific expression in the cotton genome.
Udall J, et al. “A Novel Approach for Characterizing Expression Levels of
Genes Duplicated by Polyploidy,” Genetics: 173:1 (2006).
Applications
and
References
10 |

NimbleGen Products and Services for High-Definition Genomics
NimbleGen Arrays and Services
Roche NimbleGen offers two options to fit your schedule,
budget, and focus: order arrays to perform experiments in
your own lab or send us sample and let us perform the
experiment for you. Applications include:
CGH (Comparative Genomic Hybridization)
Measure DNA copy number differences between a test and
reference genome.
ChIP-chip (Chromatin Immunoprecipitation-on-chip)
Measure transcription regulation, the histone code,
polymerase activity, or any DNA-protein binding.
DNA Methylation
Correlate promoter and genic DNA methylation with gene
expression and compare differential methylation between cells,
tissues, and other research samples, such as tumor samples.
Gene Expression
Profile genome-wide gene expression patterns to study
effects of treatments or causes of variations in eukaryotic
or prokaryotic organisms.
Sequence Capture
Enrich large regions or thousands of loci from complex
genomic DNA in preparation for high-throughput sequencing.
Custom Arrays
Accelerate your development of new and cutting-edge
scientific applications.
Instruments
Increase throughput while achieving high quality,
reproducible results.
Kits
Simplify the experimental process with prepackaged
reagents and validated protocols.
Software
Facilitate the research pipeline from array design to image
extraction to data analysis with our suite of software.
Training
Receive detailed instruction in both the theory and
practice of genomic and epigenomic research techniques
at our customer workshops, at our facility or yours.

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Other brands or product names are trademarks of their respective holders.
For life science research only.
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