Microsatellite STR Analysis

Figure 1: 18 Microsatellite Loci

Microsatellite genotyping is the genotyping of tandem repeats such as Short Tandem Repeats (STRs) or Variable Nucleotide Tandem Repeats (VNTRs). STRs and VNTRs are polymorphic DNA loci present throughout the genome. Microsatellite genotyping is a widely accepted tool for a variety of applications such as linkage mapping studies, association studies, and identification of organisms.

Applied Biosystems' five-dye chemistry increases the number of microsatellite markers that can be run in a single capillary, for improved throughput. Figure 1 is an example of 18 microsatellite loci co-electrophoresed in a single capillary.

Products
Experimental Workflow: Find the Products You Need for Every Step
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Step 1: DNA Purification

DNA extraction is a critical first step in the experimental workflow of DNA Sequencing and Fragment analysis. The overall quality, accuracy and length of the DNA sequence read can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction.

Products for Step 1: DNA Purification

MELT™ Total Nucleic Acid Isolation System

Stop homogenizing tissue samples. With the MELT Total RNA Isolation System, tissue samples are quickly and easily lysed in MELT solution. The RNA in the resulting lysate is stable for days at room temperature or longer at lower temperatures. Isolate the RNA using magnetic bead-based separation technology.

RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Tissues

Extract total RNA or DNA from formalin- or paraformalin-fixed, paraffin-embedded (FFPE) tissues. This kit enables the molecular analysis of archived tissue samples at both the genomic and gene expression levels. With this kit, nucleic acid is obtained that is suitable for qRT-PCR, mutation screening, and microarray analyses.

NucPrep® DNA Chemistry for Tissues

Starter kit for DNA isolation from animal and plant tissues and cells, etc., using NucPrep® Chemistry.

MagMAX™ Express Magnetic Particle Processor

MagMAX™ Express magnetic particle processors are ideal for researchers who want to automate their MagMAX sample preparation kits. The MagMAX Express platform is the premier automated platform to meet your throughput needs.

MagMAX™ Express-96 Magnetic Particle Processors

MagMAX™ Express magnetic particle processors are ideal for researchers who want to automate their MagMAX sample preparation kits. The MagMAX Express platform is the premier automated platform to meet your throughput needs.

Step 2: Primer Design & PCR Amplification

Amplify region of interest with fluorescently labeled primer pair.

Products for Step 2: Primer Design & PCR Amplification

Thermocycler Systems

Custom Labeled Primers

Step 3: Sample Prep for Fragment Analysis Run

Add aliquot of PCR reaction to size standard and Hi-Di Formamide mix; heat denature and proceed with electrophoresis.

Products for Step 3: Sample Prep for Fragment Analysis Run

Hi-Di™ Formamide

Highly deionized formamide used to resuspend samples before electrokinetic injection in capillary electrophoresis systems.

GeneScan™ Size Standards

GeneScan™ Size Standards are fluorescently-labeled DNA fragments required for performing fragment analysis and genotyping applications on our capillary electrophoresis platforms.

Step 4: Capillary Electrophoresis

During capillary electrophoresis, the products of the cycle sequencing reaction are injected electrokinetically into capillaries filled with polymer. High voltage is applied so that the negatively charged DNA fragments move through the polymer in the capillaries toward the positive electrode.

Products for Step 4: Capillary Electrophoresis

3500 Genetic Analyzer

The 3500 8-capillary platform can run a wide variety of applications—including de novo sequencing and resequencing (mutational profiling)—as well as microsatellite analysis, MLPA™, LOH, MLST, AFLP® and SNP validation or screening. The majority of applications can be run on a single polymer and capillary array.

3500xL Genetic Analyzer

The 3500xL 24-capillary platform can run a wide variety of applications, including de novo sequencing and resequencing (mutational profiling), as well as microsatellite analysis, MLPA™, LOH, MLST, AFLP® and SNP validation or screening. The majority of applications can be run on a single polymer and capillary array.

3730 DNA Analyzer

The 48-capillary 3730 DNA Analyzer is the Gold Standard in medium-to-high throughput genetic analysis. Use this for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Get the highest quality data at a low cost per sample. This is upgradeable to 96 capillaries.

3730xl DNA Analyzer

The 96-capillary 3730xl DNA Analyzer is the Gold Standard for high throughput genetic analysis. Use this for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Get the highest quality data at a low cost per sample.

3130 Genetic Analyzer

Applied Biosystems 3130 Genetic Analyzer is the latest generation of 4-capillary electrophoresis instruments for the low to medium throughput laboratories. The system offers industry-leading performance, plus sophisticated automation capabilities allowing you to save time, reduce costs and increase productivity.

3130xl Genetic Analyzer

Applied Biosystems 3130xl Genetic Analyzer is the latest generation of 16-capillary electrophoresis instruments for the medium throughput laboratories. The system offers industry-leading performance, plus sophisticated automation capabilities allowing researchers to save time, reduce costs and increase productivity.

310 Genetic Analyzer

The ABI PRISM® 310 Genetic Analyzer is an automated single-capillary genetic analyzer designed for a wide range of sequencing and fragment analysis applications.

Step 5: Data Analysis

Downstream analysis software will size and genotype the collected data.

Products for Step 5: Data Analysis

GeneMapper® Software

GeneMapper is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems.
Literature
Fact Sheet
- Microsatellite Analysis on the Applied Biosystems 3130 Series Genetic Analyzers