Affymetrix GeneChip Expression

DNAVision is an Affymetrix official service provider since 2003 for the GeneChip® series of products. GeneChip®-based genome-wide expression profiling is available to both academic and industrial customers. Several thousands of GeneChip® and several hundreds of projects have been successfully run to completion

We provide a complete service program based on the Affymetrix GeneChip®, giving our customers access to the latest technologies, without them having to invest heavily in resources.

We provide a comprehensive range of support - from guidance in study design, experiment planning and laboratory work, to data analysis and mining, and preparation of publications.

We are not a simple service provider but a real partner providing added value to your research.

Full Expression Profiling

Starting from very low quantity of total RNA (from 5 ng), we can run very robust and cost effective protocol to give you the confidence and turn-around time critical for a successful experiment.

Description of the work flow :

A) Sample reception

Incoming samples (frozen, fresh or FFPE sample or total RNA) first undergo a visual QC.

Then, if needed, RNA is extracted in RNase free environment from any eukaryotic (animals or plants) sample stored in the following conditions

Fresh or Frozen Samples in RNAlater (or equivalent)
Frozen Samples
Frozen cutting slides of Samples in OCT cryoembedding media
Samples in Trizol (or equivalent)
FFPE Samples
Bacteria
PaxGene Blood Samples

Quantitation and estimation of RNA purity is performed using NanoDrop spectrophotometer readings at 260 and 280 nm (according to the labeling protocol, from 5 ng of total RNA is required for the eukaryotic samples and 10 µg from prokaryotic samples)

Finally, RNA integrity is assessed using Agilent 2100 Bioanalyzer to measure RNA integrity number (RIN) A RIN of 7.5 is required for non-FFPE samples.

B) Labeling / hybridization and scanning

Target preparation utilizing either :

3' In Vitro Transcription for non FFPE RNA samples

3' IVT Express Kit from 50 ng of Total RNA
One-Cycle Target Labeling and Control Reagents from 1 µg of Total RNA
Ovation™ RNA Amplification System V2 et le FL-Ovation™ cDNA Biotin Module V2 from 5 ng of Total RNA
Prokaryotic Target Labeling Assay from 10 µg of total RNA
WT-Ovation™ FFPE System V2 from 50 ng of Total RNA

3' In Vitro Transcription from Blood Sample with Globin Reduction

One-Cycle Target Labeling from 6 µg of Total RNA
Two-Cycle Target Labeling from 3 µg of Total RNA

Whole Transcript Analysis (Exon arrays)

WT Sense Target Labeling from either 100 ng or 1 µg (without or with Ribosomal RNA reduction)

Array hybridization, washing, and scanning followed by array QCs
Sending of the final report including QCs analysis report and the intensities of each gene.
To ensure security, all information is provided in an electronic form on a DVD. Encryption is available on request. Data may also be delivered by secured dedicated web site.

C) Quality Control

As recommended by Affymetrix, several quality controls (QC) are performed while processing the samples. These QCs include spike-in controls or in-process sample controls. After image processing, a detailed QC report is generated and sent along with the results. Thus you’ll be informed about any potential bias before performing statistical analysis of your data

The MicroArray Quality (MAQC) Project

The MicroArray Quality Consortium (MAQC) project (http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/), is a community-wide effort that aims to provide quality control tools to the microarray community in order to avoid procedural failures and to develop guidelines for microarray data analysis by providing the public with large reference datasets along with readily accessible reference RNA samples.

The results of phase 1 of the MAQC project, published in the September 2006 Nature Biotechnology special issue (http://www.nature.com/nbt/focus/maqc/index.html) have shown, between other things, that gene expression measurements showed inter- and intraplatform reproducibility.

The second phase of the MAQC project is primarily focused on predictive classifiers (signatures) for health outcomes based on microarray data. DNAVision has used its in-house developed tools (bioinformatics) for the quality control analyses of phase 2 datasets.

D) Available Arrays

GeneChip® Human Genome U133 Plus 2.0 Array	GeneChip® Arabidopsis ATH1 Genome Array
GeneChip® Human Exon 1.0 ST Array	GeneChip® Barley Genome Array
GeneChip® Mouse Genome 430 2.0 Array	GeneChip® Citrus Genome Array
GeneChip® Mouse Exon 1.0 ST Array	GeneChip® Cotton Genome Array
GeneChip® Rat Genome 230 2.0 Array	GeneChip® Maize Genome Array
GeneChip® Rat Exon 1.0 ST Array	GeneChip® Medicago Genome Array
GeneChip® Rat ToxFX 1.0 Array	GeneChip® Poplar Genome Array
GeneChip® C. elegans Genome Array	GeneChip® Rice Genome Array
GeneChip® Drosophila Genome 2.0 Array	GeneChip® Soybean Genome Array
GeneChip® Xenopus laevis Genome 2.0 Array	GeneChip® Sugar Cane Genome Array
GeneChip® Xenopus tropicalis Genome Array	GeneChip® Tomato Genome Array
GeneChip® Yeast Genome 2.0 Array	GeneChip® Vitis vinifera (Grape) Genome Array
GeneChip® Zebrafish Genome Array	GeneChip® Wheat Genome Array
GeneChip® E. coli Genome 2.0 Array	GeneChip® Canine Genome 2.0 Array
GeneChip® P. aeruginosa Genome Array	GeneChip® Chicken Genome Array
GeneChip® Plasmodium/Anopheles Genome Array	GeneChip® Porcine Genome Array
GeneChip® S. aureus Genome Array	GeneChip® Rhesus Macaque Genome Array