Quality Control of Nucleic Acids Analysis with Agilent Bioanalyzer and Fragment Analyzer

The Core Facility staff offers analysis of nucleic acid samples (both RNA and DNA) using both the Agilent 2100 Bioanalyzer and Agilent (formerly AATI) Fragment Analyzer. This instrument provides an objective measure of nucleic acid quality that is more informative and more sensitive than traditional agarose gel results, without the use of toxic ethidium bromide and with reduced run times. Both systems combine gel-filled (micro)-capillaries, microfluidics and voltage induced separation with laser induced fluorescence detection of the analyzed nucleic acids. Neither instrument will provide information about chemical contaminants such as phenol, salts, proteins, ethanol etc. They provide limited information on the concentration of a sample and they are not recommended if an accurate concentration is required for a downstream application.

The user provides samples at the required concentration and will fill out a service request form located in a folder at the right of the Core entrance. Core Facility staff will run the samples and email the results to the user in an easily viewable PDF file format. The output for each instrument will be a pseudo-gel, and for each sample a separate electropherogram and a results table. Please submit your samples in 1.5 ml tubes labeled the researchers initial consecutive numbers and the date and keep your samples frozen, especially RNA samples.

Analysis can usually be arranged within 2 business days.

Analysis with Agilent Bioanalyzer

The Bioanalyzer is used predominantly to analyze the integrity of RNA, based among other parameters on the ratio between 28 and 18S rRNA. Depending on the chip, total RNA at concentrations between 25-500 ng/ul (Nanochip), 50-5000 pg/ul (Picochip) can be reliably detected. Lower concentration may be detected by each chip, depending on the size distribution of the RNA. Up to 12 samples can be analyzed at a time on the Nanochip and up to 11 samples on the Picochip. Samples should be suspended/diluted in water or less than 10 mM Tris, pH 7.0- 7.5.  Depending on the quality of the RNA sample a summarizing quality score, the so called RIN score will be calculated by the software.

The Bioanalyzer can also be used to detect the size distribution of dsDNA using different chips depending on the application. Please contact the core for details if you are interested in this service.

Quality Control with Fragment Analyzer

The Fragment Analyzer is the Genomics Core’s preferred instrument to analyze the size distribution for dsDNA for applications as NGS library QC or cloning. It can reliably and simultaneously determine the size (1 to several thousand base pairs) and proportional distribution of up to 10 dsDNA samples with a concentration between 3-10 ng/ul. Samples should be resuspended/diluted in 10 mM Tris, pH 7.0-7.5 or water.

For more information or to request service, please contact the director of the Genomics Core, Christoph Schorl (Christoph_Schorl@brown.edu, 401-863-2875).