MICROARRAY CORE SERVICES

Gene Expression Profiling

The microarray core offers a gene expression profiling method that utilizes the high density oligonucleotide of Affymetrix.There are two types of expression arrays: the 3'-Expression array ( underline 3'-Expression array with the hyperlink to: http://www.affymetrix.com/products/arrays/index.affx) and the new Exon and Tiling array. We currently service only the 3'-expression array. If there are enough interest in the Exon and Tiling arrays, please let us know.(link emailto dnguye@lsuhsc.edu).

RNA Sample Preparation

Total RNA is the preferred target.  In our experience,  RNA prepared based method (ie. Qiagen RNeasy) using a column is the preferred method. In certain cases, RNA prepared using the Trizol reagent followed by additional purification using a column (Qiagen RNeasy) yields RNA that produces satisfactory microarray data. Other methods or modifications are also suitable. Please inquire if you are uncertain as to whether an RNA extraction method that you are considering, is suitable.

Quality Control

Two quality control measures are carried out on a small aliquot of the submitted RNA samples:
(1) a spectrophotometric analysis using the NanoDrop ND-1000 UV-Vis Spectrophotometer to confirm the concentration and to detect proteins contaminants; 
(2) a size fractionation procedure using either the Nano or Pico RNA Chip assay (Agilent Bioanalyzer) to determine whether the RNA is intact. We will notified the investigator if any of the samples failed these tests.

Submitting RNA Samples

We offer two levels of service for the 3'-Expression arrays that is dependent on the amounts of starting concentration of total RNA. 

Service A:1 - Single IVT - If a minimum of 5ug of total RNA is available. Ideally the RNA should be in a total volume of 10 ul, giving the concentration of 0.5ug/ul. We also request that an aliquot of the sample be submitted along with the stock sample. We will use this to assess for RNA integrity and concentration.

Service A:2 - Double IVT- If the starting RNA is limiting, especially from microdissection or clinical samples, we can carry out an amplification step. From our experiences, the minimal amount is 100ng of high quality total RNA.

Service B - Hybridization of labeled cRNA to the Test Chip or standard GeneChip.

To get the cost for running one sample using the single IVT procedure, just add the costs for Service A1 and B.

Data Analysis

We will provide basic analysis using Affymetrix software @ $28.50 per  hour-does not include any graphics or clustering. We will provide user with lists of genes and their description that are differentially expressed between the groups using GCOS and DMT 3.0. No data mining is included. Users can use Affymetrix NetAffx (sign up is required to use their annotation tools) or use Gene2function, a web service provided by the Core.

For more sophisticated analyses, including different normalization options, analysis techniques, clustering, pathway mapping, etc. The core can provide assistance @ $75.00 per hour, or on an occasional collaborative basis
 
For users within the LSUHSC-NO, data will be deposited to a secure server, accessible only by the user's login Id.

If there is a problem...
The vast majority of the samples that passes the Quality Control measures will yield good results. However, if there is a failure, the Core will absorb costs related to problems introduced during the laboratory processing in the Core, as well as problems caused by chip defects. RNA and DNA quality/quantity problems are the responsibility of the user. Marginal cases will be discussed on a case-by-case basis with the Core Director.

 Click here for a list of our fees: Microarray Core Fees