Microarray & NGS: Frequently Asked Questions

Q: What should I do to start a project?
A: You need to contact Dr. Sridar Chittur at 518-591-7215 or schittur@albany.edu to discuss the specifics of your project, obtain a quote and establish time lines. Once the quote is accepted and a grant # or PO is assigned to the project, reagents and chips required for the study will be ordered by the Core. You can either bring your samples personally or ship it to us on dry ice. All samples should be accompanied by a completed RNA submission sheet and a picture of the gel or BioAnalyzer report.

Q: What type of arrays can the Core process?
A: Currently we offer processing of Affymetrix GeneChip arrays (prokaryotic and eukaryotic samples). We generally use standardized Affymetrix protocols. If you have a need for special services or protocols, please discuss with the Core for feasibility.

Q: What type of starting material does the Core accept?
A: We accept tissues for RNA isolation as well as user-isolated total RNA, mRNA labeled or fragmented cRNA for Affymetrix GeneChip analysis.

Q: What happens if my RNA quality is not optimal?
A: All samples submitted to the Core will be analyzed on the Agilent BioAnalyzer. If the quality of your RNA is less than optimal, the Core will contact you and ask you to make a decision regarding processing of the samples. If you ask us to process a sample which we consider of poor quality, we are not responsible for poor yields in probe synthesis or hybridization. A second probe synthesis or GeneChip hybridization will NOT be done free of charge. Please contact us if you would like more information about the type of quality measurement we perform.

Q: What if the submitted samples do not meet the Core's concentration requirement?
A: We understand that slight variations in concentrations occur when different people measure concentrations. Unless the difference between the concentrations you submit and the ones we measure are significant, we will continue with the processing. If the discrepancy is significant, you will be contacted. If the core has to manipulate the sample in order to attain the required concentrations, a per sample surcharge will be applied.

Q: How much total RNA do I need to send?

Microarray type Starting amount
Affymetrix 3´ expression 2 µg.
Affymetrix 3´ expression (small sample prep) 50 ng.
Affymetrix Whole Transcript – GENE ST 150 ng.
Affymetrix Whole Transcript – EXON ST 1.5 µg.
Nugen pico amplification 10 ng.
Affymetrix Tiling 3.5 µg.
Affymetrix microRNA 150 µg.
Agilent microRNA 150 ng.
Agilent Expression 1 µg.
Nimblegen eukaryotic gene expression 1 µg.
Nimblegen prokaryotic gene expression 10 µg.

Q: Why am I being charged for a BioAnalyzer RNA assay?
A: RNA quality is essential for gene expression analysis using microarray technology. This system allows for precise quantitation and quality assessment with small sample volume. As little as 25 ng/ul is required per analysis. RNA degradation is assessed utilizing the 28s and 18s rRNA. RNase degradation is easily detected by a shift in the RNA size distribution towards smaller fragments and a decrease in fluorescence signal of ribosomal peaks.

Q: What is your turn around time?
A: Samples are handled in the order they were received. Usually if you submit total RNA, we can send you the data within 2 weeks.

Q: What does the Core do with any leftover cRNA, probe and/or GeneChips?
A: The Core will store your starting material, cRNA and probe at -20oC for a month. GeneChips will also be stored at 4oC for a month. PLEASE COLLECT YOUR RNA, cRNA, PROBES AND GENECHIPS WHEN YOU PICKUP THE DATA. We are NOT responsible for materials left in our facility for over a month.

Q: What format of data will I receive from the Core?
A: The Core will extract data from individual chips for you. We will give you the EXP (general experimental information), DAT (image), CEL (averaged intensity), CHP (data in Affymetrix software format) and TXT (same information as in CHP but in text format for importing in to other software). A RPT (report) file containing signal data on control genes and experimental parameters will also be included for each chip. Please note that all files (expect TXT) require Affymetrix software. The RPT file can be viewed in Notepad.

Q: Can I get detailed analysis of my data?
A: The Core has computers with software licenses for Microarray Suite, Data Mining Tool (Affymetrix) and GeneSpring (Agilent). Please contact the Core for more information.

Q: I think my chip was defective? How can I be sure and what do I do?
A: Defective chips are replaced free of charge by Affymetrix. The Core will usually contact you if we suspect that your chip is defective. Affymetrix will request a copy of the DAT and EXP files for a defective chip and on confirmation, replace the defective chip. Please note that it usually takes a month for the replacement.

Q: Can I buy chips from the Core?
A: The Core can obtain chips from Affymetrix at prices significantly cheaper than list prices. We strongly urge you to avail of this opportunity and have us buy the chips for you. You may also buy the chips yourself and provide them to us prior to the study. Please note that if you provide us the chips you are responsible for obtaining the replacements for any defective chips.

Q: Can I sell any leftover chips back to Affymetrix or the Core?
A: No. Unfortunately most chips are sold in packs of 2, 6 or 30 (or packs of 5 or 30 for older arrays)which leads to leftover chips if you do not have enough samples. We realize that chips are expensive and budgets are tight. All we can suggest is teaming up with another lab to use up all the chips.


Contact Information

Core Director

Sridar Chittur, Ph.D., M.B.A

(518) 591-7215



Marcy Kuentzel, M.S.

(518) 591-7219



Guy Russo, M.S.

(518) 591-7219