Roche NimbleGen | Gene Expression

Gene Expression

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 eukaryotic, bacterial and archaeal genomes are the gene expression platform of choice as evidenced by a growing list of scientific publications.

Eukaryotic Designs represent the latest builds for human and model genomes, including rat, mouse, zebrafish, Drosophila, C. elegans, yeast, and more. Designs are available in both single and multiplex design formats, allowing for both genome-wide probe coverage and high-throughput analysis.
Bacterial Designs are available for over two hundred Class I, II, and III organisms. Because each expression microarray contains up to 385,000 probes per array with our 385K format and 72,000 probes per array with our 4x72K format, there is sufficient probe capacity to tailor an existing array design to address specific research questions.
Archaeal Designs are available for over twenty-five organisms. Because each expression microarray contains up to 385,000 probes per array with our 385K format and 72,000 probes per array with our 4x72K format, there is sufficient probe capacity to tailor an existing array design to address specific research questions.
Custom Designs allow researchers to specify their regions of interest for a fine-tiling approach or design their own targeted probes for a tailored array solution. They may be ordered for delivery (for hybridization in your own lab) for any organism.

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Advantages

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 & 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.	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)
Identify factors involved in plant tissue differentiation.	Pischke M, et al. “A Transcriptome-Based Characterization of Habituation in Plant Tissue Culture,” Plant Physiol.: 140:1255 (2006)
Microarray analysis of two S. mutans strain identified a gene responsible for biofilm formation.	Motegi M, et al. “Assessment of Genes Associated with Streptococcus mutans Biofilm Morphology,” Appl. Environ. Microbiol.: 72: 6277 (2006)
Discover regulatory targets for an orphan two-component signal regulator and virulence factor in Streptococcus pneumoniae.	Ulijasz A, et al. “Regulation of Iron Transport in Streptococcus pneumoniaeby RitR, an Orphan Response Regulator,” J Bacteriol.: 186:8123 (2004)
Study different but closely related protozoan parasites using a single expression microarray design.	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)
Tiled Expression
Register the non-coding RNAs in human fibroblasts and yeast.	Rinn J, et al. “Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Non-coding RNAs,” Cell: 129:1311 (2007)
Identify novel transcripts in rice or Populus trichocarpa.	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)
Catalog global gene expression in Homo sapiens, Drosophila melanogaster, Chlamydomonas reinhardtii, Arabidopsis thaliana, or rice.	Rinaldi C, et al. “Transcript Profiling of Poplar Leaves upon Infection with Compatible and Incompatible Strains of the Foliar Rust Melampsora larici-populina,” Plant Physiol: 144:347 (2007)
Confirm bioinformatically identified genes using expression profiling.	Tuskan G, et al. “The genome of black cottonwood, Populus trichocarpa(Torr. & Gray),” Science: 313:1596 (2006)
Catalog the global gene expression in rice.	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)

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

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

	12x135K	385K	4x72K
A. thaliana
C. elegans
D. melanogaster
Human
Mouse
Populus			CUST
Rat
S. cerevisiae
S. pombe
Zebrafish			CUST

Bacterial Designs

	12x135K	385K	4x72K*
Bacterial Designs	CUST
* 4x72K Catalog Designs are available for the following organisms: Agrobacterium tumefaciens str. C58 B. licheniformis ATCC 14580 Bacillus anthracis str. 'Ames Ancestor' Bacillus subtilis subsp. subtilis str. 168 Bacteroides fragilis NCTC 9343 Borrelia burgdorferi B31 Brucella melitensis 16M Campylobacter jejuni subsp. jejuni NCTC 11168 Clostridium acetobutylicum ATCC 824 Clostridium thermocellum ATCC 27405 Desulfovibrio desulfuricans G20 Enterococcus faecalis V583 Escherichia coli K12 Escherichia coli O157:H7 EDL933 Geobacter sulfurreducens PCA Helicobacter pylori strain G27 Klebsiella Pneumoniae (subsp. pneumoniae MGH 78578) Listeria monocytogenes str. 4b F2365 Nitrosococcus oceani ATCC 19707 Nitrosomonas europaea ATCC 19718 Nostoc sp. PCC 7120 Oenococcus oeni PSU-1 Pseudomonas fluorescens PfO-1 Salmonella enterica subsp. enterica serovar Typhi Ty2 Salmonella typhimurium LT2 Shewanella oneidensis MR-1 Staphylococcus aureus subsp. aureus COL Staphylococcus aureus subsp. aureus MW2 Streptococcus agalactiae A909 Streptococcus pneumoniae R6 Streptococcus pneumoniae TIGR4 Synechococcus elongatus PCC7942 Vibrio cholerae 01 biovar El Tor str. N16961 Yersinia pestis KIM

Archaeal Designs

	12x135K	385K	4x72K*
Archaeal Designs	CUST
* 4x72K Catalog Designs are available for the following organisms: Archaeoglobus fulgidus DSM 4304 Methanosarcina acetivorans C2A Methanosarcina barkeri str. fusaro Sulfolobus acidocaldarius DSM 639 Sulfolobus solfataricus P2

KEY:
	- Delivery AND Service Workflow
	- Delivery Workflow Only
	- Service Workflow Only
CUST	- This design is not available as a catalog design but can be ordered as a custom design. Find out more...

Literature

Brochures & Sales Flyers

NEW! Roche NimbleGen Research Solutions: Microarrays and target enrichment for genetic disease discovery
Brochure (PDF Format 7.1MB)
NimbleGen Gene Expression Microarrays
Brochure (PDF Format 4.8MB)
NimbleGen Gene Expression 12x135K Arrays
Sales Flyer (PDF Format 276KB)
NimbleGen Prokaryotic Gene Expression Microarrays
Sales Flyer (PDF Format 296KB)
NimbleGen Zebrafish Gene Expression 385K Arrays
Sales Flyer (PDF Format 361KB)
NEW! Nexus Expression Software
Sales Flyer (PDF Format 3.6MB)

User Guides

NimbleGen Arrays User’s Guide: Gene Expression Arrays (Version 6.0)
User’s Guide (PDF Format 2.4MB)

Application Notes & Technical Notes

Genome-Wide Screen of Promoter Methylation Identifies Novel Markers in Melanoma
Application Note (PDF Format 2.7MB)
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)
High-Quality Data Obtained with NimbleGen Gene Expression Arrays
Technical Note (PDF Format 125KB)

For a complete listing of literature covering all Roche NimbleGen products and services please visit our literature page.

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