Spotted Arrays - Unlabeled submissions

Submission option 1: Total RNA for Expression Analysis

Total RNA sample requirements are 40ug of total RNA at a concentration of at least 3ug/ul. While the lab will perform QC analysis of all samples submitted for microarray analysis, it is advisable that the investigator perform a preliminary assessment of sample quality before sending samples to the lab. Failure to perform standard QC analysis of your RNA samples will result in sample processing delays.

All samples and a fully completed sample submission form should be delivered to the DNA Array Lab, located in the Thomas Building, DE-740.

Labeling request forms
If you are using a FHCRC project id for billing, please fill out the Internal submission form.

If billing is to be submitted to the University of Washington or other external institution, fill out the External submission form.

Submission option 1: Preparation of Cy3 and Cy5 labeled targets directly from Total RNA

The Genomics Resource staff generates Cy3 or Cy5-labeled cDNA targets using the labelling protocol below that is appropriate for the arrays.

• Amino-allyl labeling for cDNA Arrays protocol



• Amino-allyl labeling for Oligo Arrays protocol

Samples are closely monitored throughout this process using the Agilent 2100 Bioanalyzer and the NanoDrop ND-1000 spectrophotometer.

Submission option 2: Total RNA with Amplification Requested for Expression Analysis

Total RNA sample requirements are 4ug of total RNA at a concentration of at least 0.2ug/ul. While the lab will perform QC analysis of all samples submitted for microarray analysis, it is advisable that the investigator perform a preliminary assessment of sample quality before sending samples to the lab. Failure to perform standard QC analysis of your RNA samples will result in sample processing delays.

All samples and a fully completed sample submission form should be delivered to the DNA Array Lab, located in the Thomas Building, DE-740.

Amplification form
FHCRC, Cancer Consortium members, and External users please use the sample submission form here.

The Genomics Resource staff generate Cy3 or Cy5-labeled aRNA targets for hybridization with strict sample preparation protocols outlined in the Ambion Message Amplification and Modified Amplification of RNA aa-MessageAmp protocols.

Samples will be closely monitored throughout this process using the Agilent 2100 Bioanalyzer and the NanoDrop ND-1000 spectrophotometer.

Submission option 3: aRNA with Dye-Coupling Requested for Expression Analysis

aRNA sample requirements are 6ug of aRNA at a concentration of at least 1ug/ul. While the lab will perform QC analysis of all samples submitted for microarray analysis, it is advisable that the investigator perform a preliminary assessment of sample quality before sending samples to the lab. Failure to perform standard QC analysis of your RNA samples will result in sample processing delays.

All samples and a fully completed sample submission form should be delivered to the DNA Array Lab, located in the Thomas Building, DE-740.

aRNA coupling request form
FHCRC, Cancer Consortium members, and External users please use the sample submission form here.

Submission option 3: Preparation of Cy3 and Cy5 aRNA labeled targets

The Genomics Resource staff generate Cy3 or Cy5-labeled aRNA targets for hybridization with strict sample preparation protocols outlined in the Modified Amplification of RNA aa-MessageAmp protocol beginning at the "post amplification dye coupling"step.

Samples will be closely monitored throughout this process using the Agilent 2100 Bioanalyzer and the NanoDrop ND-1000 spectrophotometer.

Submission option 4: miRNA Labeling Requested for Expression Analysis

RNA sample requirements are 7ug of Total RNA at a concentration of at least 1ug/ul. While the lab will perform QC analysis of all samples submitted for microarray analysis, it is advisable that the investigator perform a preliminary assessment of sample quality before sending samples to the lab. Failure to perform standard QC analysis of your RNA samples will result in sample processing delays.

All samples and a fully completed sample submission form should be delivered to the DNA Array Lab, located in the Thomas Building, DE-740.

miRNA labeling request form
FHCRC, Cancer Consortium members, and External users please use the sample submission form here.

Submission option 4: Preparation of Hy3 and Hy5 miRNA labeled targets

The Genomics Resource staff generate Hy3 or Hy5 labeled miRNA targets for hybridization with strict sample preparation protocols outlined in the miRCURY LNA microRNA Array Labeling Kit protocol.

Sample QC

Quality control of total RNA includes:
QC test for RNA degradation. The resource has two Agilent 2100 Bioanalyzers that are used to assess the initial RNA quality. To learn more about how to interpret Bioanalyzer results, please visit the Agilent web site.

QC test for protein and organic contaminates. The resource has a NanoDrop ND-1000 spectrophotometer that is used to assess sample purity. Employing a UV scan from 210nm - 310 nm, the following criteria must be met:

• 1.8 ≤ A₂₆₀/ A₂₈₀ ≤ 2.1
• A₂₆₀ / A₂₃₀ ≥ 1.7
• A₃₁₀ ~ 0

To ensure that the above criteria are based on sufficient absorption measurements, we also require an A₂₆₀ > 0.3 when performing this analysis.

In instances where one or more samples do not pass our initial QC tests, we will not proceed with the project and immediately contact the submitter with our findings.

Continue to next step in the process.