Genomics, Sandbox Sample Preparation

Preparing a Sample for Submission

For most applications the user supplies RNA or DNA, while the unit performs the specific processing of the sample as required, hybridization of the labeled sample to the array of choice (which is purchased directly by the user), scanning of the array, quantification of the image and basic analysis. Advanced analysis is not supplied by the unit, but can be obtained from the Bioinformatics unit.

Please bring your samples with the appropriate submission form, filled with all the details:

TapeStation samples

 

General outlines

 

  1. Unless otherwise specified, samples should be submitted in nuclease-free water. Most extraction kits supply such water.
  2. Submit your samples in 1.5 ml tubes for all applications. Make sure tubes are well labeled and that labels are easily understood.
  3. RNA samples should be submitted on ice or dry ice, but not in liquid nitrogen.
  4. When submitting samples, please print out the relevant submission form, fill it out and bring it with your samples. Samples will not be accepted without a form. * INSERT SAMPLE SUBMISSION FORMS!
  5. Required amounts and concentrations by application: When submitting your samples, make sure to follow the specifications listed below. In case of need to de viate from these figures, please consult us first.

 

TapeStation analysis

TapeStation RNA Input: Total RNA at a volume of 3µl in a concentration of 50-500 ng/ul for nano kit or 0.5-10ng/µl for pico kit

TapeStation HSDNA Input: DNA at a volume of 3µl in a concentration < 10ng/ul

RNA and DNA samples concentrations must be standardized around the same concentration in the range.

We recommend to prepare the samples for the final process [i.e sequencing], then to take an aliquot for TapeStation analysis.

 

 

Blue Pippin

Note: Reagents and Cassettes are provided by the users (available at Zotal Ltd)!

Sample should be in a 30µl TE Buffer:
Maximum Load: 10g sheared genomic DNA
2 g restriction/PCR band capture
Minimum Load: low single nanograms, sheared genomic DNA
50 ng restriction/PCR band capture
Optical Sensitivity approx. 10-15ng single bands, restriction
(Midori-Green cassettes): fragments, PCR products, or synthetic DNA fragments

Input Sample Characteristics
When running the BluePippin, characteristics of input DNA can affect separation resolution and efficiency of product recovery. The following general guidelines should be followed:

  • Ionic strength: The ionic strength of the sample should be lower than the ionic strength of the buffer (80mM monovalent ions). High salt concentrations can result in slower than expected DNA mobility.
  • Protein in the sample: DNA-binding proteins such as ligases or polymerases can affect the mobility of fragments during separation. Proteins can also reduce DNA recovery from the elution module by increasing the binding of DNA to the ultrafiltration membrane at the back of the elution module. For best results, samples should be de-proteinized prior to loading whenever possible.
  • Input DNA size distribution: A knowledge of the input size distribution is obviously important to program accurate size selection settings. BluePippin cassettes are calibrated using the Agilent Bioanalyzer to evaluate input and product sizes, and so, for best results, input size distributions should be evaluated using the Bioanalyzer. For low concentration samples, the Agilent HS chip is very useful .