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Fragment Analyzer QC
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RNA/DNA QC - Fragment Analyzer (AATI) QC

OVERVIEW - Fragment Analyzer QC (AATI)

** 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.

Fragment Analyzer QC: (back to top)

General Info. --

The Advanced Analytical Fragment Analyzer is a capillary electrophoresis based platform that provides sizing and quality control of DNA and RNA in a plate format.  

* Fragment resolution from 10bp to 40,000bp
* Resolution down to 3bp
* Detection from 5 pg/ul


§ Assays and their Applications --

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

  • DNA Assays

    * NGS Library QC

    * Large Fragment QC
    * Genomic DNA QC

  • RNA Assays:

    * Small RNA QC (5nt-200nt)

    * Standard Sensitivity RNA QC (15nt-6,000nt)
    * High Sensitivity RNA QC (15nt-6000nt)

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 Kit Type Assay Type

Size Analysis Range

* Sample Concentration
- Detection Range

• NGS Library QC (Standard Sensitivity)
• NGS Library QC (High Sensitivity)
• NGS Library QC (High Sensitivity Small Fragment)
25bp - 5,000bp
25bp - 5,000bp
50bp - 1,500bp
0.1ng/ul - 10ng/ul
5pg/u l- 500pg/ul
5pg/ul - 500pg/ul
Large Fragment
• Large Fragment QC (Standard Sensitivity)
• Large Fragment QC (High Sensitivity)
• Large Fragment 50kb QC (High Sensitivity)
50bp - 20,000bp
50bp - 20,000bp
75bp - 48,500bp
0.1ng/ul - 10ng/ul
5pg/ul - 500pg/ul
5pg/ul - 600pg/ul
• gDNA QC (Standard Sensitivity)
• gDNA QC (High Sensitivity)
• gDNA 50kb QC
50bp - 20,000bp
50bp - 20,000bp
75bp - 48,500bp
5ng/ul - 200ng/ul
50pg/ul - 5ng/ul
25ng/ul - 250ng/ul
• Small RNA
• RNA (Standard Sensitivity)
• RNA (High Sensitivity)
5nt - 200nt
15nt - 6000nt
15nt - 6000nt
50pg/ul - 2ng/ul
25ng/ul - 500ng/ul
500pg/ul - 5ng/ul

• Data Release --

The data generated from the Advanced Analytical Fragment Analyzer instrument will be emailed to you in .pdf and .xls format.

  • PDF file - contains run summary, method information, gel image, and trace for each sample.
  • Excel file - contains concentration, molarity, and size information.

• Data Analysis --

Our data interpretation guide will help you understand your data better. If you still have questions/concerns regarding your data, please feel free to contact us at panbioanalyzer@stanford.edu.

• Turn-around Time --

Orders will be processed within 2 days of submission.