Expression Profiling with Affymetrix

Starting from very small quantities of total RNA (from 5 ng), we can apply  very robust  cost-effective protocols to give you the confidence and turnaround times critical for successful experiments.

Description of the work flow :

A) Sample reception

Incoming samples. All samples received are labeled with a unique internal ID number and recorded  in a validated electronic laboratory system management database. They are checked to confirm package/sample integrity, appropriate shipping conditions (frozen samples/dry ice, where appropriate) and a confirmation of sample identity against the shipping manifest is sent by e-mail on the  day of  reception.

If necessary, RNA is extracted in an RNase free environment from any eukaryotic (animal or plant) or prokaryotic sample(see Nucleic Acid Extraction in DNAVision).

Quantification and estimation of RNA purity is performed (depending on  the labeling protocol chosen, we can start from 5 ng  total RNA)

Finally, RNA integrity is assessed using an Agilent 2100 Bioanalyzer to measure RNA integrity number (RIN).

B) Labeling / hybridization and scanning

Target preparation using Affymetrix / Nugen / Genisphere or ABI protocols:

Array hybridization, washing and scanning followed by array QCs

Sending of the final report including the QC analysis report and  intensities of each gene.

C) Deliverables and Quality Controls: BEYOND THE AFFYMETRIX QCs

While Affymetrix describes some basic quality control metrics, in parallel to our ISO17025 accreditation, we have developed via the yaqcaffy library  a semi-automated QC strategy to ensure data of high quality.As the quality of  data is key to any further analysis, in DNAVision we have validated our processes based on the MAQC consortium and  ISO17025 guidelines.

As part of our Affymetrix Expression service, you will receive:

• Raw data files
• Extracted data files:
  • a file including all the intensity values by probe_set
  • a file including the annotations provided by probe_set
• Project report :
  • Project description
  • RNA assessment data
  • Affymetrix assessment data using the yaqcaffy
  • Conclusions of the analyses if required (see below)

D) Biostatistical and bioinformatical analyses

In addition to  the core service activities carried out in a high quality environment, we can also provide you with basic to in-depth data analysis to  extract the relevant information from your data. For more details please go to Bioinformatics in DNAVision.

All  data are provided in  electronic form on a DVD. Encryption is available on request. Data may also be delivered via a  secure dedicated web site.

E) Available Catalog Arrays

We can provide you with any GeneChip Array available on the Affymetrix website (including the miRNA Array) (http://www.affymetrix.com/products_services/index.affx). Depending on  availability, we can also provide you with  custom microarrays.