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 NO GREATER than 8 microliters. 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 |
|---|---|---|---|---|
| Affymetrix One Cycle IVT Labeling** | 2ug (total RNA) |
>250 ng/ul |
8 ul |
Yes. 3ul |
| Affymetrix Two Cycle IVT Labeling** | 10-100 ng (total RNA) |
>10 ng/ul |
3 ul |
Yes. 3ul |
| Ambion MessageAmp Premier Labeling | 100-500 ng (total RNA) |
>50 ng/ul |
3 ul |
Yes. 3ul |
| Affymetrix WT Labeling with Invitrogen RiboMinus | 2 ug (total RNA) |
>500 ngg/ul |
4 ul |
Yes, 3ul |
| Ambion WT Amplification with Affymetrix WT Labeling | 100ng-500ng (total RNA) |
>50 ng/ul |
4 ul |
Yes, 3ul |
** From September 2009 Affymetrix will no longer be supplying the One Cycle IVT kit or the Two Cycle IVT kit. All new projects will be processed with the Ambion MessageAmp Premier protocol (or Affymetrix 3' IVT Express protocol). We are currently investigating alternate suppliers of the One Cycle IVT chemistry for ongoing projects that need to compare back to data generated with the Affymetrix One Cycle IVT kit. 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)