The Applied Genomic Technologies Core

Submission Guidelines for Microarray Services

Sample Submission Guidelines for RNA Quality Bioanalyzer Analysis

• Submit 3ul of total RNA at minimum concentration of 50ng/µl in PCR strip tubes.
• Submit sample information as an Excel format (see submission form and sample ID sheet) as well as an electronic copy.

Sample Submission Guidelines for Affymetrix 3' Expression Analysis

The first-time Affymetrix Expression Analysis user should consult AGTC Microarray staff and bioinformatics staff for experimental design strategy, sample preparation, target labeling protocol, type of Affymetrix array, etc. Investigator should submit total RNA samples and microarrays following the sample submission guidelines.

Isolating high quality RNA is the key to successful microarray analysis! Since the most appropriate protocol for the isolation of RNA can be source dependent, we recommend using a protocol that has been established for the tissues or cells being used. In the absence of an established protocol, using one of the commercially available kits designed for RNA isolation is suggested. When using a commercial kit, follow the manufacturer’s instructions for RNA isolation.

• Submit 100-500ng of total RNA at a minimum concentration of 33ng/µl in 10 µl.
• RNA needs to have an A260/A280 ratio of 1.9-2.1.
• Integrity of samples will be determined by the core using an Agilent 2100 Bioanalyzer. Investigators will be notified if samples are of poor quality.
• Submit sample information as an Excel format (see submission form and sample ID sheet) as well as an electronic copy.

Sample Submission Guidelines for Affymetrix Whole Transcript Sense Target Labeling Assay

• Submit 100-500ng total RNA at a minimum concentration of 33ng/µl in 10 µl for Exon 1.0 ST and Gene 1.0 ST array analysis.
• RNA needs to have an A260/A280 ratio of 1.9-2.1.
• Integrity of samples will be determined by the core using an Agilent 2100 Bioanalyzer. Investigators will be notified if samples are of poor quality.
• Submit sample information as an Excel format (see submission form and sample ID sheet) as well as an electronic copy.

Sample Submission Guidelines for Affymetrix Prokaryotic Expression Analysis

• Submit 10-11 µg of total RNA at a minimum concentration of 0.56 µg/µl.
• RNA needs to have an A260/A280 ratio of 1.8-2.1
• Integrity of samples will be determined by the core using an Agilent 2100 Bioanalyzer. Investigators will be notified if samples are of poor quality.
• Submit sample information as an Excel format (see submission form and sample ID sheet) as well as an electronic copy.

Sample Submission Guidelines for Affymetrix miRNA Array Analysis

• Submit 1-2 µg of total RNA at a minimum concentration of 0.125 µg/µl.
• RNA needs to have an A260/A280 ratio of 1.8-2.1
• Integrity of samples will be determined by the core using an Agilent 2100 Bioanalyzer. Investigators will be notified if samples are of poor quality.
• Submit sample information as an Excel format (see submission form and sample ID sheet) as well as an electronic copy.

Sample Submission Guidelines for Affymetrix Tiling Array Analysis

• Submit 7-10 µg of total RNA at minimum concentration of 1 µg/ul in 10 µl.
• RNA needs to have an A260/A280 ratio of 1.8-2.1
• Integrity of samples will be determined by the core using an Agilent 2100 Bioanalyzer. Investigators will be notified if samples are of poor quality.
• Submit sample information as an Excel format (see submission form and sample ID sheet) as well as an electronic copy.

Sample Submission Guidelines for Affymetrix Resequencing Analysis

Genomic DNA or PCR products can be submitted for Affymetrix Resequencing Analysis.

• Submission of Genomic DNA
• DNA should be high quality (purified). The A260/A280 ratio should be close to 1.8.
• Submit 15 µl of each sample at 5ng/µl in molecular biology grade water.
• Submit samples in the same type of 96-well plate.
• Submit sample information as an Excel format (see submission form and sample ID sheet) as well as an electronic copy.
• DNA concentration will be determined by core using Quant-it pico green assay. The investigator will be notified if DNA concentration is lower than 5ng/µl.
• Submission of PCR products
• All PCR reactions should be optimized and products visualized by gel electrophoresis before submission.
• 25-50 µl of each individual PCR reactions should be submitted.
• Submit samples in the same type of 96-well plate.
• Submit sample information as an Excel format (see submission form and sample ID sheet) as well as an electronic copy.
• PCR products will be quantified by the Core using Quant-IT pico green assay. The investigator will be notified if the concentration of the PCR product is not sufficient.

Sample Submission Guidelines for Other Affymetrix Arrays, Agilent DNA Microarray and Spotted Arrays

For other types of samples, glass slide including Agilent DNA microarray and custom spotted glass arrays, or Affymetrix arrays, please contact the AGTC Microarray for guidance Zhen Zhang (518) 474-6992.