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RNA/DNA QC - Agilent Bioanalyzer QC

OVERVIEW - Agilent Bioanalyzer QC

** QC for RNA/DNA samples can be done on two different machines: Agilent Bioanalyzer QC and Advanced Analytical Fragment Analyzer. Both platforms provide comparable results.

** Please check out the differences below to determine which machine is best suited your needs. Please contact us at panbioanalyzer@stanford.edu if you are unsure.

Agilent Bioanalyzer
Fragment Analyzer (AATI)
microfluidics-based with the lab-on-chip technology 96 capilllary eletrophoresis
min/max samples per order
no limit per order minimum 48 samples to maximum 95 samples per order (last well is reserved for ladder)
Sample submission
Individual tubes or plate Plate format only
$ per sample $ per plate

up to 10 Kb

up to 48 Kb


Data output includes: total RNA concentration and RNA integrity number (RIN).

Data output includes: total RNA concentration and RNA quality number (RQN).

Small RNA

Sample: Resolution of single stranded RNA fragments up to 150nt.

Sample: Distinguishes between the microRNA region (10-40nt) and small RNA region (10-200nt). 

The RNA Integrity Number (RIN) is a score on a scale of 1-10 used to approximate the integrity of total RNA.  This score accounts for presense or absence of degraded products and is often used as a quality metric to determine the viability of total RNA for an experiment. The RNA Quality Number (RQN) is an assesment of the quality of total RNA using a 1-10 scale and can be compared to the BioAnalyzer RIN score.

** You must also check the submission requirements for each machine before placing your orders.



General Info. --

The Agilent 2100 Bioanalyzer is a microfluidics-based platform, and with the lab-on-a-chip technology, it can provide sizing, quantification and quality control of DNA, RNA, proteins and cells in a short period of time. Each Agilent chip contains an interconnected set of microchannels that is used for separation of nucleic acid fragments or proteins based on their size as they are driven through it electronically.

§ Assays and their Applications --

     PAN Facility currently offers different assays for a wide range of applications:

  • DNA Assays (DNA 1000 and High Sentivity DNA): provide sizing and quantification of DNA fragments and DNA smears down to pg/ul sensitivity.

  • RNA Assays:
    Total RNA Assay
    (Eukaryote, Plant, Prokaryote)
    provides RNA quality check with RIN (RNA Integrity Number), a quantification estimate and ribosomal ratios for total RNA and mRNA samples.
    mRNA Assay
    provides a quantitation estimate and percentage of rRNA contamination. No RIN provided.

  • Small RNA Assay: provides verification and optimization of miRNA after extraction procedures; analyzes miRNA directly in total RNA or in enriched samples; compares small RNA regions in extracts and tissues; separate miRNA from other small RNAs.

Please use the following table as a guide to choose the right assay for your samples. Before submitting your samples, you must also check out the concentration requirements for the assay chosen since each assay has different sensitivity level.

Starting Material Sample Type Assay Type

Size Analysis Range

* Sample Concentration
- Detection Range

dsDNA, cDNA, genomic DNA, NGS DNA
• DNA 1000
• High-Sensitivity DNA
25 - 1000 bp
50 - 7000 bp
Total RNA, mRNA, cRNA, fragmented RNA, microRNA
• Nano RNA (Eukaryote, Plant, Prokaryote)
• Pico RNA (Eukaryote, Plant, Prokaryote)
• Small RNA (6-150 nt)
25 - 4000 nt
25 - 4000 nt
6 - 150 nt
* Although the Bioanalyzer is capable of detecting the lowest concentration amounts shown, we would recommend to have your sample(s) in the higher detection range for better results.

• Data Release --

The data generated from the Agilent 2100 Bioanalyzer will be emailed to you in .pdf format and/or .xad format.

  • PDF file - contains run summary, assay details, electropherogram, gel image, result tables and the ladder info. The sample will be named as such, 'your initials'_'sample name'.

  • XAD file - is raw data file, which can be viewed using the free, downloadable Agilent 2100 Expert Software. This software allows you to manipulate the data at the regions of interest (specifically useful for DNA assays). For details about the sofware and what you can use it for, click here.

• Data Analysis --

Our data interpretation guide will help you understand your data better. For further analysis of your samples, you can use the Agilent 2100 Expert Software to open the raw (.xad) data file. If you still have questions/concerns regarding your data, please feel free to contact us at panbioanalyzer@stanford.edu.

• Turn-around Time --

Samples are usually processed within 24 hours and they will be disposed off after all successful runs. In case of any leftover and sample returned is requested, samples will be put back in freezer and kept for one week for you to come back and pick them up. After that, everything will be disposed of.