For IRRI scientist only: Fluidigm System

 Single nucleotide polymorphism (SNPs) markers are a powerful tool for genetic studies. The Fluidigim System enables efficient, high-throughput processing of SNP genotyping samples with increased speed and  reproducibility. 

The Fluidigm array is an integrated fluidic circuit (IFC) that have a network of channels and valves that route reagents and samples into chambers and assemble them automatically. 
At GSL we work with the Fluidigm EP1 System. 

If you want to see how this system works, please watch the video below.

 At the GSL, we are currently offering  two different arrays: 192.24 Dynamic Array and 96.96 Dynamic Array.

Fluidigm 96.96 Dynamic Array

This array provides the flexibility of a microwell plate and the density of a microarray in one. At the GSL, the Fluidigm 96.96 array, can be run with fixed sets of 
96 SNPs markers for diversity analysis and rapid variety group identification, or with custom sets of 96 polymorphic SNPs for QTL mapping and Molecular-Assisted Back-crossing (MABC).

See pool of SNP markers available.

Fixed sets of SNPs have the lowest cost, while users who want to run custom sets of assays will have to bear the cost of preparing the new sets of markers for running. In addition, those having exclusive SNPs (that are not in our panel set) will need to purchase these assays first, and then have a surcharge to cover both the initial primer preparation and the cost of preparing new sets of markers for running.

Fluidigm 124.24 Dynamic Array 

This array provides the ideal solution for high sample throughput SNP genotyping. It is designed to genotype 192 samples against 24 SNP arrays in a single run.

At the GSL, the Fluidigm 124.24-SNP chip is aimed towards deployment of small sets of fixed and custom SNP markers across large populations for fine mapping and breeding applications. Specialized “breeder’s chips” will be developed with fixed sets of targeted trait-specific SNP markers for each breeding program.

As with the 96.96 Dynamic array, custom and exclusive marker orders will have added surcharges.

If you want to submit samples, please follow these guidelines.

Data Analysis

For the SNP Data Analysis, each year the GSL offers a workshop that allows participants to become familiar with the different software and online tools for SNP analysis such as Flapjack, Powermarker, QGene, TASSEL, and Structure.

In this link you can download some of the software tools that we use for the analysis of data.