Sample Submission Requirements:

RNA isolation and sample submission

Recommendations for RNA isolation for Affymetrix GeneChip hybridization assay can be found in the Genomics Core Sample Preparation document. Samples may be submitted for amplification and biotin-labeling in the Genomics Core lab or already labeled. Protocols for RNA sample labeling can be found in the Affymetrix GeneChip Expression Analysis Technical Manual (copies available in the Genomics Core facility and GMSR Bioinformatics Suite).

Sample submission for labeling

If samples are being submitted for labeling, please follow these guidelines:

Amount of RNA:

A minimum of 8 ug of total RNA or 0.5 ug of polyA+ RNA must be submitted for each sample. We encourage larger amounts of RNA whenever possible, especially for first time users of the microarray core facility. RNA must be submitted to the core facility in aqueous solution (preferably RNase-free water), frozen on dry ice.

RNA Sample Details:

Please provide an electronic copy (e-mail or disk) (email address is genomics@gwu.edu) of an Excel spreadsheet with the following information for each RNA sample (head columns with titles in bold):

• Name of sample (maximum 6 alphanumeric characters that will be useful to you for identifying and tracking sample)
• RNA type (e.g. total RNA or poly A+RNA)
• OD260 /OD280 ratio
• Concentration (ug/ml)
• Total volume (ml)

In addition, please provide a gel photo showing size distribution of RNA samples (with markers). Please indicate type of gel and concentration.

Post-labeling submissions

If samples are being submitted after amplification and labeling, please follow these guidelines:

Amount of RNA:

A minimum of 15 ug of biotinylated cRNA target must be provided at a concentration of, at least, 0.6 ug/ml in RNase-free water for QC testing and one genome array hybridization. For multiple genome array hybridizations, additional material is required. Please contact Core personnel to determine the amount of labeled target required.

Target Details

Please provide an electronic copy (e-mail or disk) of an Excel spreadsheet with the following information for each sample (head columns with titles in bold):

• Name of sample (maximum 6 alphanumeric characters that will be useful to you for identifying and tracking sample)
• Starting amount of RNA used for cDNA synthesis
• RNA type (e.g. total RNA or poly A+RNA)
• Yield of biotinylated cRNA (unadjusted)
• Concentration of biotinylated cRNA (ug/ml)
• Total volume of biotinylated cRNA

In addition, please provide a gel photo showing size distribution of biotinylated cRNA (with markers).

Data Analysis

Affymetrix Microarray Suite (MAS) software will be used to analyze the array image for each sample following hybridization, washing and staining. A spreadsheet with MAS
globally scaled data for each sample will be provided to you, along with MAS image and unscaled data files. In addition, we can also provide a limited number of pairwise comparisons of any two samples using the Affymetrix software. If you would like to utilize this option, please indicate samples to be compared below.

Please provide the following information for each comparison:
Comparison # Baseline/Control Sample Comparison Sample