9/27/2024: The guidelines to submit samples for DNA/RNA Size QC have recently changed.
 The DNA/RNA Size QC assays require samples to fall within a recommended concentration range. You may need to dilute the material that you submit to have a concentration within the range of the assay.

Step 1: Determine the concentration of your samples

First, determine the concentration of your primary samples. For accurate quantification, we recommend using a Qubit or other intercalating dye (with standards), or a Nanodrop/Quickdrop spectrophotometer if the sample concentration is > 30ng/ul.

Step 2: Prepare aliquots to submit for size QC

For optimal results, submit samples with concentration near the high end (but not above) the recommended concentration range. Please see below for tips about volume and vial requirements.

Fragment Analyzer

Sample concentrations submitted for size QC on the Fragment Analyzer should fall within the range of the “high sensitivity” assay:
    DNA samples    0.25 – 5 ng/ul
    RNA samples    1 - 5 ng/ul (recommended: 3-5ng/ul for optimal detection)

If your original samples have concentration > 5ng/ul, please prepare an aliquot diluted to ≤ 5 ng/ul to submit for size QC. If your original samples have concentration > 250 ng/ul and require > 50-fold dilution, prepare an intermediate stock and confirm the concentration with a Nanodrop/Quickdrop or Qubit before preparing the final aliquot diluted to ≤ 5 ng/ul. Samples do not need to be diluted to exactly the same concentration, as long as the final aliquots for all samples fall within the range of the assay.

• Example 1: Sample concentration = 100 ng/ul. Prepare an aliquot consisting of 1 ul primary sample + 19 ul nuclease-free water (1:20 dilution to final 5 ng/ul).
• Example 2: Sample concentration = 1000 ng/ul. Prepare an intermediate stock by combining 2 ul sample + 18 ul nuclease-free water (1:10 dilution), and check the concentration as dilutions highly concentrated primary stocks may not perform as predicted. If you observe that the intermediate stock has concentration 125 ng/ul, prepare a final aliquot consisting of 1 ul intermediate stock + 24 ul nuclease-free water (1:25 dilution to final 5ng/ul).

Femto Pulse

This instrument is used to profile high molecular weight genomic DNA samples (concentration range: 50-500 pg/ul) , or low concentration RNA samples (25-250 pg/ul). Samples must be diluted to the appropriate concentration range as indicated.

Warning about high concentration samples

We typically do not confirm the concentration of samples submitted for size QC. Loading samples with concentrations above the maximum listed can affect the results of the entire run, and may incur additional charges to rerun your samples and any others affected in the same run.

Volume requirements

Please provide at least 5 uL of each sample within the recommended concentration range. Extra volume will not be returned. If you cannot provide 5 uL, please consult with the Genomics Facility before submitting your samples.

Vial requirements

We accept samples in individual 0.5-1.5mL tubes, PCR strip tubes, or PCR plates. We do not accept samples in individual 200ul PCR tubes. When submitting more than 5 samples, PCR strip tubes or plates is preferred. For RNA samples, use RNAse-free vials.

• Tubes: individual 500ul or 1.5mL tubes, preferably screw cap vials from VWR (catalog # 16466-052) or USA Scientific (catalog # 1405-9700, 1405-9706, and 1450-9799).
• PCR strip tubes: any PCR strip tubes with secure caps. Please number the tubes, not the lids, to match the order of samples listed in the order form.
• Plates: any PCR-style 96-well plates (i.e. not with a flat or round bottom). Please fill plates across by row and leave the last column (col 12) empty (e.g A1-A11, then B1-B11, etc). Include the well position of each sample in the sample name or comments when placing the order. If shipping plates, we highly recommend using strip-caps as sealing film may become dislodged or leak during shipment.