Roche NimbleGen provides a unique combination of high-density arrays, long-oligo probes, and flexible design capability that together provide superior results for advanced gene expression analysis. NimbleGen microarrays enable accurate, sensitive, and specific interrogation of genome-wide expression for any sequenced and annotated genome. Researchers also can tile through a genome at any desired spacing to discover genome-wide expression activity in both coding and noncoding regions and map transcripts with unparalleled accuracy. NimbleGen microarrays and services for both prokaryotic and eukaryotic genomes are the gene expression platform of choice as evidenced by a growing list of scientific publications.
Our extensive catalog of gene expression array designs contains the major eukaryotic model organisms and over two hundred prokaryotic organisms. In addition to our standard 385K array format, Roche NimbleGen offers two multiplex formats, 4x72K and 12x135K, to ensure complete genome coverage of both small prokaryotic and large eukaryotic genomes without compromising information content or data quality. You can choose to process and hybridize your samples in your lab using our optimized protocols and reagents. Alternatively, send your samples to us for processing in our full-service laboratory, results guaranteed.
Multiplex Options: A cost-effective solution for high sample throughput
NimbleGen multiplex arrays enable you to analyze statistically meaningful populations for alterations in expression levels of annotated genes. We offer a 4-plex format (4x72K) with 72,000 probes per array and a 12-plex format (12x135K) with 135,000 probes per array. Hybridize four or twelve independent samples or run replicate samples on a single slide and average the data for increased statistical confidence.
Up-To-Date Microarray Designs
Roche NimbleGen's digital microarray manufacturing process is fast and inexpensive, allowing you to get any sequenced genome on an array rapidly. All designs are built from the latest published genomes to ensure your experiment is current.
High Information Content: Multiple probes per transcript enhance confidence in results
Ultra-high density NimbleGen arrays (385,000 and 2.1 million probes) allow every gene to be represented by multiple, unique probes. The averaging of the signal from multiple probes provides improved statistical confidence, reducing the impact of inconsistent probe behavior and improving the signal-to-noise ratio compared to platforms that offer fewer probes per gene.
Long Oligos: Long oligonucleotide probes enhance the accuracy of your analysis
NimbleGen has an unmatched ability to synthesize high-density arrays of long oligos. For gene expression analysis, long oligos (60mer) provide superior signal-to-noise ratio, increased sensitivity, specificity, and discrimination, particularly in complex eukaryotic genomes. Another significant advantage: long probes eliminate the need for mismatch probes, effectively doubling array capacity.
Great Inter-Array Reproducibility
NimbleGen arrays are manufactured to exacting standards and undergo rigorous quality control to ensure superior array-to-array data reproducibility. In replicate hybridization experiments, inter-array r2 values routinely exceed 0.98.
Expression Analysis Software
ArrayStar® software from DNASTAR, Inc. enables scientists and researchers to open and analyze normalized data (.call, .calls and .txt files) generated from Roche NimbleGen’s Expression arrays.
Applications and References
Take advantage of the inherent flexibility, sensitivity, and discrimination provided by NimbleGen Gene Expression microarrays for numerous applications.
Applications
References
Differential Expression
Study gene expression related to multiple signal pathways in tissues and cells.
Roche NimbleGen offers three array formats for our Gene Expression products:
12x135K - Running on our recently launched HD2 platform, 12x135K offers 12 arrays per slide with 135,00 probes per array.
385K - Our industry standard 385,000 probe format provides gene expression arrays with the highest information content on the market
4x72K - Four individual samples may be hybridized and analyzed simultaneously on each array with 72,000 probes.
Specifications
NEW! 12x135K
385K
4x72K
Number of Arrays per Slide
12
1
4
Total Number of Probes
12 x
135,000
385,000
4 x 72,000
Probe Length
60mer
60mer
60mer
Number of Probes per Target*
3 - 12
6 - 20
2 - 7
Number of Replicate Probe Sets per Array*
1 - 2
1 - 4
1 - 3
Feature Size
13 x 13μm
16 x 16μm
16 x 16μm
Array Size
8.9 x
6.5mm
17.4 x 13mm
7.8 x 5.7mm
Slide Size
1 x 3 in. (25 x 76 mm)
* Depending on transcriptome size.
Availability
12x135K, 385K, and 4x72K array formats are not available for every Gene Expression array design. Please consult the Availability Guide on this page for more information.
Customer Workflows
Gene Expression Delivery Workflow
Customers can purchase catalog arrays or custom arrays from Roche NimbleGen and perform the array experiments at their own laboratories or core facilities. NimbleGen arrays are synthesized on standard-sized glass microscope slides, compatible with many microarray scanners. NimbleGen arrays are optimized to provide the best performance when processed using NimbleGen instruments and reagent kits. NimbleGen provides a complete user’s guide to support customers with sample processing, array hybridization, scanning, data extraction and analysis. We also offer a training program to get you up and running with NimbleGen arrays quickly.
Gene Expression Service Workflow
Roche NimbleGen's gene expression microarray service consists of the following steps:
Customer selects catalog array design, or works with Roche NimbleGen bioinformatics scientists to design a custom array.
Customer supplies RNA or cDNA. To ensure sufficient sample for quality control analysis as well as optimum hybridization, we require the following amounts of total RNA, mRNA, or cDNA:
Total RNA*
mRNA*
cDNA
Eukaryote
20μg
5μg
2.5μg
Class I Prokaryotes
20μg
-
2.5μg
Class II and III Prokaryotes
30μg
-
5μg
*Please note that the NimbleGen procedure for sample processing does not include RNA amplification.
Roche NimbleGen performs the expression hybridization, scans the array, extracts the data, and performs a preliminary data analysis.
Roche NimbleGen delivers the following data and software to customer:
Microarray Design Files
Probe Sequences
Gene Descriptions
Raw Data Files
Normalized Data Files
Availability
Delivery and Service workflows are not available for every Gene Expression array design. Please consult the Availability Guide on this page for more information.
Availability Guide
The 12x135K, 385K, and 4x72K array formats and the Delivery and Service workflows are not available for every Gene Expression array design. Use the table below to identify the availability of different formats and workflows across our Gene Expression design offerings.
Eukaryotic Designs
Prokaryotic Designs
Custom Designs
Eukaryotic Designs
12x135K
385K
4x72K
Arabidopsis thaliana
Caenorhabditis elegans
Drosophila melanogaster
Human
Mouse
Populus
CUST
Rat
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Zebrafish
CUST
Prokaryotic Designs
12x135K
385K
4x72K*
Prokaryotic Designs
CUST
* 4x72K Catalog Designs are available for the following organisms:
What are the advantages of the Roche NimbleGen multiplex array formats?
The NimbleGen 12x135K and 4x72K array formats allow simultaneous hybridization of 12 or 4 samples, respectively, on a single slide. You can conveniently run either replicates of the same sample or multiple samples on the same slide, thus improving interarray reproducibility and reducing cost.
How many features are on each array of a Roche NimbleGen multiplex slide?
Each array on the NimbleGen 4x72K slide has 72,000 features and each array on the 12x135K slide has 135,000 features.
Do you offer multiple probes per transcript in the NimbleGen multiplex formats?
Yes, each transcript is interrogated by 3 or more probes, depending on the complexity of the organism. Please see our catalog for more details for each organism.
What kind of controls do you include on each array to ensure accurate sample loading and to confirm the integrity of the experiment?
Each array contains probes for Sample Tracking Controls (STCs) that are used for the following purposes:
a) To identify the samples after hybridization; each labeled cDNA sample is spiked with a unique Sample Tracking control before loading.
b)To ensure that there is no sample mix up between arrays.
Do all arrays on a Roche NimbleGen multiplex slide have the same design?
Yes. Currently all the arrays on a gene expression multiplex slide have identical designs.
Array Design
Do you include microRNAs or non-coding RNA in your catalog designs for expression?
Currently, no microRNA or non-coding RNA regions are used for NimbleGen gene expression array designs.
What is the probe length in gene expression arrays?
Yes, we offer both catalog and custom array designs for differential expression analysis. Please check our website for the current catalog. If you do not see your organism, please contact the Account Manager for your region to discuss a custom design.
Are your gene expression probes designed with a 3' bias?
Yes, probes are designed with some 3' bias. Our expression arrays are designed by first determining the transcript terminator as annotated in NCBI. We then take 1500bp upstream of that location and design our probes within that region.
Which strand is represented on the array?
The sense strand is represented on our arrays.
Can Roche NimbleGen design a custom expression tiled array for my specific research needs?
Yes, Roche NimbleGen can design and deliver to you custom tiled expression microarrays with probe spacing and probe length that best fits your experimental goals. Please contact your local sales representative to discuss a custom design.
Are Roche NimbleGen designs up-to-date with the latest genome builds?
Yes, Roche NimbleGen technology allows the rapid production of new array designs based on the latest genome builds.
Are designs based on earlier genome builds available?
What is the recommended protocol for isolating RNA?
We recommend the RNeasy Mini Kit (Qiagen, Cat. No. 74104) or the TRIzol Reagent (Invitrogen, Cat. No. 15596-026)). If using TRIzol-isolated RNA for cDNA synthesis, it is beneficial to perform a secondary cleanup step using RNeasy Mini Kit. Immediately after the ethanol precipitation step in the TRIzol procedure, proceed with the RNeasy Mini Kit according to the manufacturers recommendations.
Can I use a different RNA isolation method than recommended?
Any RNA isolation method that provides RNA which meets the purity and integrity criteria outlined by NimbleGen can be used.
How do you assess the quality of RNA and cDNA samples?
Pure and intact RNA and cDNA should have A260/A280 and A260/A230 ratios of at least 1.8. Additionally, they should appear intact when analyzed by gel electrophoresis or using a Bioanalyzer (Agilent).
How much RNA or cDNA do you need for gene expression analysis?
This depends on whether you are sending the samples to Roche NimbleGen for full service or if you are doing the experiment in your lab, and whether your sample is from eukaryotes or prokaryotes. When performing experiments in your lab using the Roche NimbleGen-recommended protocol, 10 μg total RNA, 1 μg mRNA, or 1 μg cDNA is required. For service, the amounts required are listed in the table below.
Total RNA*
mRNA*
cDNA
Eukaryote
20μg
5μg
2.5μg
Class I Prokaryote
20μg
-
2.5μg
Class II and III Prokaryotes
30μg
-
5μg
*Please note that the Roche NimbleGen procedure for sample processing does not include RNA amplification.
What is the expected cDNA yield from 10μg total eukaryotic RNA?
Using our standard protocol, we routinely get at least 5μg cDNA from 10μg total RNA.
If I do not have 10μg of RNA, what method for RNA amplification can I use, and can I submit the cDNA samples for full service?
cDNA synthesis methods that have been validated to perform well with NimbleGen eukaryotic gene expression service are listed below, together with the starting total RNA amount. Roche NimbleGen will also accept cDNA from amplified eukaryotic RNA. Please see the recommended RNA amplification kits below.
TransPlex® Whole Transcriptome Amplification Kit (Sigma, cat. no. WTA1) with 50 ng total RNA
TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma, cat. no. WTA2) with 50 ng total RNA
RiboMultiplier™ Sense-RNA Amplification Kit (Epicentre, cat. no. RM80510) followed with dsDNA Conversion Kit for RiboMultiplier™ sRNA (Epicentre, cat. no. RMD80625) with 100 ng total RNA
Ovation® RNA Amplification System V2 (NuGEN, cat. no. 3100) with 20 ng total RNA
WT-Ovation™ Pico System (NuGEN, cat. no. 3300) with 20 ng total RNA
These cDNA preparation methods have NOT been validated for prokaryotic samples.
What kind of samples are recommended for hybridizing on NimbleGen gene expression arrays?
We recommend using Cy3-labeled cDNA sample on our gene expression arrays. Please contact technical support for your region to obtain a recommended protocol for preparing Cy3-labeled cDNA.
Data Analysis
What method of normalization does NimbleGen use for gene expression?
We normalize expression data using quantile normalization. See Bolstad B, et al. (Bioinformatics, 19:185-193, 2003), A comparison of normalization methods for high density oligonucleotide array data based on bias and variance.
How does NimbleGen generate gene calls from gene expression arrays?
Gene calls are generated using the Robust Multichip Average (RMA) algorithm. See Irizarry R. et al. (Biostatistics 4:249-264, 2003), Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
What software do you recommend for further analysis of gene expression data?
NimbleGen provides gene expression values in calls file that can be conveniently imported into multiple gene expression analysis software such as ArrayStar (DNAStar). Currently, with the purchase of a full service project, you will obtain a 30-day demo version of ArrayStar along with your data. Array delivery customers can also request this 30-day demo version from NimbleGen.
Can NimbleGen gene expression data be used with publicly available software packages?
Several analysis packages that have been used with NimbleGen gene expression data are:
1. NMPP: Described in Bioinformatics (2006); 22: 2955 - 2957
2. MeV: Described in J. Exp. Biol. (2007); 210: 1507 - 1517.
3. R: Available at www.bioconductor.org, requires data in XYS format.
Array Service
How much RNA or cDNA do you need for gene expression analysis?
Total RNA*
mRNA*
cDNA
Eukaryote
20μg
5μg
2.5μg
Class I Prokaryote
20μg
-
2.5μg
Class II and III Prokaryotes
30μg
-
5μg
*Please note that the NimbleGen procedure for sample processing does not include RNA amplification.
When I use NimbleGen full service option, what deliverables will I receive ?
NimbleGen delivers the following data files and software to full service customer:
- Microarray Design file containing probe sequences (ndf)
- Gene Description file (ngd)
- Raw Data files (calls and pair)
- Normalized Data files (RMA_calls and RMA_pair)
Array Delivery
Can I purchase NimbleGen arrays for use in my own lab or core facility?
Yes, all catalog designs currently listed on NimbleGen website and any custom design are available for delivery.
What kits are available for use with NimbleGen microarrays?
NimbleGen offers One-Color DNA Labeling Kits, Hybridization kits, and Wash Kits to facilitate efficient and specific hybridization to our expression arrays. See our Kits & Consumables web page for more details about these kits.
What resolution scanner do I need?
The NimbleGen MS 200 scanner set at 5 micron resolution is optimal for 385K arrays. The NimbleGen MS 200 scanner set at 2 micron resolution is optimal for 2.1M arrays.
Can I scan NimbleGen arrays using my Agilent scanner?
The 5 micron Agilent scanner can work with NimbleGen arrays.
What software do I need to extract my data from a scanned image?
Roche NimbleGen’s NimbleScan software can be used to perform feature extraction from scanned images.
Does NimbleGen offer training for array delivery customers?
Yes, Roche NimbleGen Workshops are intensive, 2 to 4-day training programs designed to provide instruction in both the theory and practice of genomic and epigenomic research techniques using Roche NimbleGen high-density DNA microarrays. Click here to find out more.
When I order microarrays from NimbleGen, what deliverables will I receive?
For microarray orders, NimbleGen delivers the following items to the customer:
- NimbleGen arrays
- User’s Guide
- Microarray Design file containing probe sequences (ndf)
- Gene Description file (ngd)
How much sample do I need to run one microarray analysis in my lab?
When using NimbleGen-recommended protocol for cDNA synthesis and labeling, 10 μg total RNA, 1 μg mRNA, or 1 μg cDNA is required for each array.
