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.

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:

1. Customer selects catalog array design, or works with Roche NimbleGen bioinformatics scientists to design a custom array.
2. 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.

3. Roche NimbleGen performs the expression hybridization, scans the array, extracts the data, and performs a preliminary data analysis.
4. Roche NimbleGen delivers the following data and software to customer:
   • Microarray Design Files
   • Probe Sequences
   • Gene Descriptions
   • Raw Data Files
   • Normalized Data Files

Partner Solutions

Identification of differentially expressed genes can be carried out with DNASTAR’s ArrayStar software which is compatible with NimbleScan data files.

ArrayStar is an easy-to-use gene expression analysis software package that provides powerful visualization and analytical tools, and now also offers the optional QSeq® application for RNA-Seq, ChIP-Seq, miRNA, and transcriptome analysis.

Brochures & Datasheets

• NimbleGen Gene Expression Microarrays
  Brochure (PDF Format 4.8MB)
• NimbleGen Gene Expression 12x135K Arrays
  Datasheet (PDF Format 276KB)
• NimbleGen Prokaryotic Gene Expression Microarrays
  Datasheet (PDF Format 296KB)
• NimbleGen Zebrafish Gene Expression 385K Arrays
  Datasheet (PDF Format 361KB)

User Guides

• NimbleGen Arrays User’s Guide: Gene Expression Analysis (Version 5.1)*
  User’s Guide (PDF Format 1.6MB)
• * DO NOT reference this User's Guide if you are performing sample labeling using the discontinued version of the One-Color DNA Labeling Kit (Catalog Number: 05223555001) . The labeling protocols in this User Guide WILL NOT WORK with the discontinued kit. To access the labeling protocols for discontinued DNA Labeling Kits go to the DNA Labeling Kits Product Notice page and download the previous version of the User Guide.

Application Notes & Technical Notes

• NEW! Roche cDNA Synthesis System for use with NimbleGen Gene Expression Microarrays
  Technical Note (PDF Format 844KB)
• Evaluation of RNA amplification methods for NimbleGen Gene Expression microarray analysis
  Technical Note (PDF Format 1.3MB)
• Genome-Wide Screen of Promoter Methylation Identifies Novel Markers in Melanoma
  Application Note (PDF Format 2.7MB)
• High-Quality Data Obtained with NimbleGen Gene Expression Arrays
  Technical Note (PDF Format 125KB)