Genomics & Bioinformatics Core Facility

Agilent 2100 Bioanalyzer System

Sample Preparation & Submission

To ensure successful results, the sample must be of sufficient purity and appropriate concentration. We recommend using only purified products. Purity of the sample is very important for accurate size determination; high salt concentration and enzymes is known to affect the mobility of the sample. Selecting the appropriate kit is concentration dependent. See the Assay Kit table for sample type and concentration range. We recommend using a spectrometer, such as the Nanodrop, to determine sample concentration prior to submission.

Selecting the appropriate kit is sample type and concentration dependent. Refer to the descriptions of Bioanalyzer Kits and Assays for sample type and concentration range. We recommend using a spectrometer, such as the Nanodrop, to determine sample concentration prior to submission.

Complete the Sample QC Order Submission Form. For each sample to be analyzed, provide only an aliquot of 2ul in a labeled 1.5ml tubes. We strongly recommend providing an aliquot, not the primary stock. All tubes must be labeled on the side with PI Name, Date (MM/DD/YYYY), Concentration, and unique Sample Name. CORES orders will be prepared and submitted by our facility personnel.

Email the Submission Form to genomics@nd.edu. Please include in your e-mail the date and approximate time you will be delivering your samples to the Genomics Core Facility.

Genomics Core Facility
Galvin Life Science Center Room 019
Phone: (574) 631-1902

Results

The 2100 Expert Software generates user-friendly PDF report detailing the results, shows an electropherogram, and gel image for each sample. RIN numbers and sizing information is reported when appropriate. To better assist and meet your needs, we evaluate and offer a general interpretation of the results. For further discussion and explanation of results, contact usAgilent Technologies 2100 Bioanalyzer System is a complete solution for DNA/RNA quality control of limiting materials. The micro-capillary electrophoresis based technology provides high quality digital reporting of size range and quantity in a single platform. Bioanalyzer system has the resolution and power to quantify a few picograms with as little as a couple microliters of sample. As the leading standard in literature for nucleic acid quality control, 2100 Bioanalyzer is an ideal choice.

About The Bioanalyzer Chip System

Bioanalyzer chip are similar to traditional agarose gel electrophoresis in principle, but offer greater advantages. First, the amount of sample needed is considerably lower than traditional methods. For DNA, sensitivity of detection ranges from 5pg to 50ng. For RNA, 0.5ng to 500ng is sufficient for analysis.

Analysis of the sample is simple and reliable. First, interconnected micro-channels nested within the Bioanalyzer chip are primed with a polymer containing an intercalating fluorescent dye. Next, samples are loaded with a marker into each well of the chip. Electrophoretic current is applied to the chip, driving size separation of the nucleic acids. As the sample migrates, fluorescent intensity is recorded, and the data is translated into electropherogram (peaks) and gel-like image (bands).

2100 Expert Software

The 2100 Expert Software provides reliable, quick analysis of your sample and generates user-friendly detailed reports. Pre-loaded analysis protocols are available for many sample types: total RNA, messenger RNA, small RNA, and fragmented DNA (i.e.. cDNA, PCR products, and restriction-digested/fragmented DNA). With the simple click of a button, the software reports the concentration, fragment sizes, and molarity for each sample. Advanced protocols and tools allow for custom analysis to evaluate size ranges/distributions.

What is the RNA Integrity Number (RIN)?

RNA Integrity Number (RIN) is a comprehensive measure of RNA quality. The RNA Integrity Number uses several parameters to assess and rate on a scale of 1 to 10 RNA quality of a typical ribosomal pattern. The RIN may not be applicable to all samples, especially those with atypical ribosomal RNA patterns.

2100 Bioanalyzer Kits and Chip Assays

The 2100 Bioanalyzer DNA/RNA kits are designed to meet the needs of most sample types. Genomics DNA is not supported. DNA Kits are designed to accommodate fragmented DNA (i.e.. cDNA, PCR products, and restriction-digested/fragmented DNA). RNA Kits are designed for analysis of Total RNA and mRNA from eukaryote, prokaryotes, and plants. Typically, kits process up to 12 samples per run. Low input kits* accommodate only 11 samples. Note: The small RNA kit** is supported, but not kept in stock.

 
Fragmented DNA
DNA Assay Kits
Conc. Range ng/ul
Size Range (bp)
DNA 7500
1 - 50
100 - 7500
DNA 1000
1 - 50
25 - 1000
DNA High-Sensitivity*
0.005 – 0.5
50 - 7000

 

 
Total RNA
mRNA
RNA Assay Kits
Conc. Range ng/ul
Size Range (bp)
Conc. Range ng/ul
Size Range (bp)
RNA 6000 Nano
5 – 500
50 - 6000
25 – 250
50 - 6000
RNA 6000 Pico*
0.05 – 5
50 - 6000
0.025 – 5
50 - 6000
Small RNA**
0.05 – 2
6 – 150
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Examples of Illumina Libraries

[Coming Soon]

Examples of PCR Products

[Coming Soon]

Examples of Total RNA Results of Varying Quality

High-Quality Total RNA with a typical ribosomal RNA profile: Intact, High Quality Total RNA
  • Flat baseline
  • Cleanly separated ribosomal peaks
  • Little to no sloping between peaks

 


 

 

Low-Quality Total RNA with a typical ribosomal RNA profile: Partially Degraded Total RNA

  • Baseline rises
  • Ribosomal peaks merge
  • Inter ribosomal peaks appear
  • Size shift begins towards lower end

Extremely Low-Quality Total RNA with a typical ribosomal RNA profile: Severely Degraded Total RNA
  • Ribosomal peaks gone
  • Small size indicates severe fragmentation

 

Examples of High-Quality Total RNA with Atypical Ribosomal Patterns

The following examples demonstrate that the 2100 Bioanalyzer software is unable to determine the RIN value because of the atypical ribosomal patterns. Regardless, a trained and skilled technician is capable of evaluating and interpreting the results.

 

Apis mellifera Total RNA

 

Hyallela azetca Total RNA

 

Nasonia vitripennis