Affymetrix GeneChip Sample Submission Requirements

Affymetrix® GeneChip® Sample Submission Requirements

  • For submission of samples that will be labeled and arrayed, please submit RNA that has been resuspended in nuclease-free WATER ONLY in a volume of 5-8ul. For the minimum starting amount of RNA required please see the table below.
  • All samples will have a quality check before arrayed. Please provide an extra 3ul aliquot of each sample in a separate tube for this quality analysis.
  • ***Please note: It is critical that the QC tube has the same concentration as the sample tube.***
  • Samples will be checked on NanoDrop for concentration and for the 260/280 and 260/230 absorbance ratios. Samples will also be checked using the Agilent Bioanalyzer for RNA integrity.

Target Labeling Services

Processing Type Starting Amount Starting Concentration Starting Volume Extra QC Sample Required
Ambion MessageAmp Premier Labeling 100-500 ng (total RNA) >50 ng/ul 3 ul

Yes. 3ul

Ambion WT Amplification with Affymetrix WT Labeling 100ng-500ng (total RNA) >50 ng/ul 4 ul Yes, 3ul
Affymetrix FlashTag Biotin HSR Labeling (Affymetrix miRNA array) 1ug (total RNA) >125ng/ul 8ul

Yes, 3ul

NuGEN Ovation Pico WTA System V2 1ng-5ng (total RNA) >0.1ng/ul 3ul-10ul Yes, 3ul
Affymetrix GeneChip WT Pico 1ng-10ng (total RNA) >0.5ng/ul 3ul Yes, 3ul

Please contact us at microarraylab@duke.edu if you have any questions.

Post Target Labeling Services

Processing Type Starting Amount Starting Concentration Starting Volume Extra QC Sample Required
NuGEN Fragmentation and Labeling of NuGEN WT amplified product for Exon GeneChip Hybridization at least 5ug (cDNA) 170ng/ul - 330ng/ul 27 ul Yes, 3ul*
Fragmented cRNA for GeneChip Hybridization 20 ug (cRNA) 0.5 ug/ul >40 ul >No
Fragmented and Labeled cDNA for GeneChip Hybridization
(NuGEN, all varieties)
Follow appropriate protocol Follow appropriate protocol >50 ul >No

*Please submit 3ul of the ssDNA elution in one tube for QC (to ensure absence of contamination), and submit the remainder of the ssDNA elution (~27ul) in a separate tube for the fragmentation and labeling protocol. (See NuGEN WT-Ovation Pico System User Guide Step IV, I, 14-17, for elution information. Click here for product page.)