Sample Submission Form

Overview:

Currently, the StemCore Microarray Facility offers Affymetrix  Genechip Technology®  for gene expression and DNA Analysis profiling. This technology provides efficient access to genetic information using miniaturized, high-density arrays of oligonucleotide probes. If sample quantity is limited, current protocols in place allow us to process samples that are at concentrations as low as 50 ng/µl. Quality assessment measures for total and mRNA samples are available. Use of the Agilent Bioanalyzer for this purpose is strongly recommended for each sample submitted and can be indicated on the request form. This service can also be requested for RNA that will not be utilized for a GeneChip experiment.

Equipment:

• GeneChip Hybridization Oven (64 GeneChip capacity)
• Two Fluidics Stations (12 GeneChip capacity in one 8 hour shift)
• Scanner (36 GeneChip capacity in one 8 hour shift)

Services Provided:

We are pleased to announce that we are now able to provide access to the full line of Affymetrix Gene Expression and DNA Analysis products including:

• miRNA Array
• Human Gene 1.0 ST
• Human Exon 1.0 ST
• Human Promoter 1.0R
• Mouse Gene 1.0 ST
• Mouse Exon 1.0 ST
• Mouse Promoter 1.0R
• Rat Gene 1.0 ST
• Rat Exon 1.0 ST
• New Model Organism Chips (Xenopus, Zebrafish, C.elegans etc.)
• 500K SNP Mapping Assay Chip
• Tiling Arrays

Technical specifications regarding the full Affymetrix product line can be found at www.affymetrix.com

Process:

• Samples from local researchers should be dropped off at the Microarray Facility Monday-Friday between the hours of 9:00 AM and 4:00 PM along with a fully completed Request Form. Please make sure to indicate RNA concentration for each sample and ensure that the label on the tube exactly matches the sample name given on the request form.
• Samples from external sources should be shipped to the above mailing address via Federal Express or Purolator to the attention of Caroline Vergette. In advance of shipment of the RNA samples please fax the completed request form to Caroline Vergette at (613) 739-6294. If your RNA sample has been obtained from human subjects, please include a copy of the appropriate ethics review approval forms. The samples should be shipped on dry ice to the Stemcore Laboratory (see address below). It is important to label the sample "Perishable". Please also include a copy of the previously faxed request form with the shipped samples.
• Results can generally be obtained within 2 working weeks from date of submission.
• All samples are processed on a first come first served basis.
• Laboratories will be charged for all reactions processed barring any technical issues encountered
• When your experiment has been completed you will receive an email informing you that your experiment is complete. Your results which include the Affymetrix files (.exp, .dat, .cel, and .chp) as well as a .txt file of probeset values as well as a quality assessment analysis will be saved to CD and be available for your retrieval (Ottawa customers) or sent to you by Federal Express (please provide an account number) or by Canada Post.

Fees:

Please refer to the attached fee schedule for specific services offered and associated costs. This schedule is applicable to academic researchers only. Commercial researchers should inquire for pricing and availability.

RNA Sample Preparation:

Best results are obtained using 100 ng of recently isolated total cellular RNA utilizing the whole transcript ST Labeling protocol.

The method of isolation that produces the best results in our hands is Qiagen RNeasy Mini Kit (P/N 741104). The RNA should be resuspended in RNase free water. Please do not resuspend  samples in buffers containing SDS, or other detergents, as they will inhibit the enzymatic reactions used to synthesize the target cDNA.

Reaction Submission Format:

In order to minimize error and reduce turnaround time we will only accept samples that are provided in the following format:

• Each sample should be provided in a 1.5 ml microfuge tube.
• Please provide a separate aliquot of the sample if both Affymetrix microarray analysis and Agilent Bioanalyzer quality assessment is required
• The microfuge tube should clearly be labeled with black indelible ink with the sample name as well as the requestor’s initials.

• Please ensure that the name on the microfuge tube corresponds exactly to the name indicated on the request form.
• Reaction Specifications:
                   

  Item	Concentration	Volume
  Total RNA, 1.0 ST Arrays	100ng/µl	5.0µl
  Total RNA, Exon and Tiling 1.0R Array	0.3 µg/µl	34 µl
  IP'd Double-Stranded DNA for Promoter 1.0R	15 µg	<78 µl
  IP'd Double-Stranded DNA for Tiling 2.0R Array (7 Arrays)	27 µg	<118 µl
  Genomic DNA for 10K and 100k for Mapping	50 ng/µl	20 µl

   *For arrays not listed above, please inquire.

Affymetrix GeneChip Technical Variability