Department of Botany & Plant Sciences

DNA/RNA Quality and Quantity

 DNA AND PROTEIN ANALYSIS AND QUANTIFICATION

Agilent 2100 Bioanalyzer (operated by core staff as a service)

Bioanalyzer

 

 
  Applications

The Agilent 2100 Bioanalyzer is used to assess the quality and quantity of DNA and RNA templates for Illumina sample prep but can be used to examine any nucleic acid or protein for mass, purity or degradation.

  • DNA size and quantity
    High-resolution separation and quantification
  • RNA quality check with RIN for mammalian samples
    The industry standard for RNA analysis offering total RNA, mRNA, and small RNA data including RIN algorithm (RNA Integrity Number). There are RIN values available for plant samples as well.
  Specifications
  • The instrument uses microfluidics contained within a chip for electrophoresis of small sample quantities.
  • Fluorescence signals are converted to gel-like images with either bands or peaks as output.
  • A variety of commercial analysis chips are available for the instrument.
 

Available kits and submission
The charge is per chip, not sample number. One microliter of sample is loaded per sample. For submission please provide at least 2ul. In addition, please provide a Nanodrop or Qubit quantification at time of submission. Submission forms are available on line at the IIGB Reservation and Billing Site. For prices per chip see our service Rates page. Available kits and their specifications are listed below.

Agilent RNA 6000 Nano Kit (PN 5067-1511)
12 samples/chip
Quantitative 25-500 ng/ul
Qualitative 5-500 ng/ul
Buffer compatibility: 100 mM Tris or 125 mM NaCl or 15 mM MgCl2

Agilent RNA 6000 Pico Kit (PN 5067-1513)
11 samples/chip
Quantitative +/- 30% accuracy
Qualitative 50-5000 pg/ul
Buffer compatibility: 50 mM Tris or 50 mM NaCl

Agilent Small RNA Kit (PN 5067-1548)
11 samples/chip
Quantitative 25% CV
Qualitative 50-5000 pg/ul
Max. Buffer concentration: 10 mM Tris and 0.1 mM EDTA

Agilent DNA 1000 Kit (PN 5067-1504)
12 samples/chip
Quantitative 0.1-50 ng/ul
Sizing range 25-1000bp
Max. Salt Concentration: 250 mM for KCl or NaCl, 15 mM for MgCl2

Agilent DNA High Sensitivity Kit (PN 5067-4626)
11 samples/chip
Quantitative 5-500 pg/ul
Sizing range 50-7000bp
Max. Buffer concentration: 10 mM Tris and 1 mM EDTA

  Advanced Analytical Fragment Analyzer

(operated by core staff as a service)

  Applications

The applications of the Fragment Analyzer are similar to those of the Agilent 2100 Bioanalyzer to assess the quality and quantity of DNA and RNA templates for Illumina sample prep. The advantages of the Fragment Analyzer are:

  • Higher throughput. The Fragment Analyzer uses capillary electrophoresis. Our instrument uses 12 capillaries and can thus analyzer a single row (12 samples) of a 96-well plate or can do entire 96-well plates. Thus, it is ideal for larger projects.
  • DNA size and quantity. The Fragment Analyzer can access the the size of high molecular weight genomic DNA up to 40,000bp, whereas the Bioanalyzer is limited to less than 10,000bp. Thus the Fragment Analyzer can be used to assess DNA shearing by Corvaris or other methods. The Fragment Analyzer also generates a trace and virtual gel image to assist with data.
  • RNA quality check. As with the Bioanalyzer the Fragment Analyzer can assign the equivalent of a RIN value.
  • Fragment analysis. As a capillary instrument the Fragment Analyzer can be used for genotyping, SSRs, microsatellites or sizing PCR fragments.
  Specifications
  • The instrument uses capillary electrophoresis for separation permitting a wider range of size selection
  • Fluorescent dyes to stain DNA/RNA are converted to gel-like images with either bands or peaks as output.
  • A variety of commercial analysis kits are available for the instrument.
  Available kits and submission
The charge is per 12 samples (one row of a 96 well plate), not sample number. Submission forms are available on line at the IIGB Reservation and Billing Site. For prices per chip see our service Rates page.Two microliter of sample is diluted and loaded per sample well. For submission please provide at least 3ul. In addition, please provide a Nanodrop or Qubit quantification at time of submission. Submission forms are available on line at the IIGB Reservation and Billing Site. For prices per 12 samples, see our Rates page. Available kits that we stock and their specifications are listed below.

 

 High Sensitivity Genomic DNA Analysis Kit
Sample volume required 2ul
Samples per run 12-capillary 11 + 1 well DNA ladder
Total run time 50 minutes

Sizing range 50bp – 40,000bp

gDNA concentration 50pg/ul – 5ng/ul

gDNA quantification accuracy +/- 25%

gDNA quantification precision +/- 15% CV

 

dsDNA Analysis Kit

Sample volume required 2ul

Samples per run 12-capillary 11+1 well DNA ladder

Total run time 28 mins

Sizing range 1bp – 500bp

DNA concentration range 0.5ng/ul – 50ng/ul

Resolution 5bp @300 bp

DNA sizing accuracy +/- 5%

DNA sizing precision +/- 2% CV

 

Standard Sensitivity RNA Analysis Kit

Sample volume required 2ul

Samples per run 12-capillary 11+1 well DNA ladder

Total run time 40 mins

Qualitative range (per smear) 5ng/ul – 500ng/ul

Quantitative range (per smear) 25ng/ul – 500ng/ul

Quantification accuracy +/- 20%

Qualtification precision +/- 10% CV

 

High Sensitivity NGS Fragment Analysis Kit

Sample volume required 2ul

Samples per run 12-capillary 11+1 well DNA ladder

Total run time 50 mins

Separation resolution 25bp – 100bp <10%; 100bp – 2000bp <5%;

2000bp – 5000bp <10%

Sizing accuracy +/-5%

Sizing precision 2% CV

DNA fragment concentration range 5pg/ul – 500pg/ul

DNA smear concentration range 50pg/ul – 5000pg/ul

Quantification accuracy +/- 25%

Quantification precision 15% CV

Max DNA concentration 500pg/ul per fragment; 5000pg/ul total

 

Additional Kits

Other kits are available for specific size ranges for quantitative and qualitative measurements including: Large fragment analysis, Small RNA analysis and qualitative kits for DNA sizing. For more information see the Advanced Analytical web site.

 

  These instruments operated by Core staff s a service. For more information or consultation about your individual applications, please contact Core Staff.
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