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Technologies

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The IGBMC “Microarray and Sequencing Platform” houses several cutting edge equipments dedicated to large scale gene analysis. While most of these resources are exclusively used by the facility staff, few machines are accessible by platform users (for IGBMC members only, please see restricted area).

High throughput sequencing

C-bot

C-bot_large.jpg The C-bot is a stand-alone, software-controlled system for the automated generation of clonal clusters from single DNA molecules on HiSeq 4000 flow cells.

HiSeq 4000

HiSeq-2000_large.jpg The HiSeq 4000 is an imaging and fluidics system for ultra-high-throughput sequencing of clonal clusters generated by the C-bot.

High throughput nanofluidics

Biomark HD System

biomark_large.gif The Biomark HD system is a high-throughput real-time PCR instrument developed by Fluidigm which relies on nanofluidics technology for sample and reagents handling. Up to 9216 PCR reactions may be carried out in parallel inside integrated fluidic circuits (IFCs), some miniaturized devices made of tens of thousands of fluid control valves and interconnected channels.

Our complete system consists of one Biomark HD Reader for thermal cycling and fluorescence detection and two IFC controllers, MX and HX, for loading samples and reagents inside the IFCs.

Using dedicated IFCs, the system supports many applications including gene expression, genotyping, mutation detection, copy number variation, or absolute quantitation of nucleic acid sequences. To date, users on our Platform have mostly performed gene expression analyses using a wide variety of sample types and various PCR chemistries (Evagreen, TaqMan® Probes, Roche Universal ProbeLibrary).

C1™ Single-Cell Auto Prep System

The C1™ system provides an easy and reproducible platform to capture and process up to 96 individual cells for subsequent RNA or DNA analysis. So far, only RNA analyses have been completed on our Platform.

Using dedicated IFCs, researchers can extract, reverse transcribe and amplify RNA in single cells. C1™ output samples are subsequently processed either on the Biomark HD system using real time PCR technology for specific targets quantification, or on the Illumina HiSeq 2500 using RNA-Seq technology for whole transcriptome analysis.

Microarrays

Affymetrix GeneChip Instrument System

GeneChip® Hybridization Oven 640

The Oven automates the hybridization process for up to 64 probe arrays at one time, while providing precise temperature and cartridge rotation control.

GeneChip® Fluidics Station 450

The station, consisting of 4 independent modules, operates selected fluidics scripts under the control of GeneChip Operating Software for probe arrays washing and staining. Conductivity measurement and real time detection with mechanical and optical sensors ensure that fluidic operations are completed successfully.

GeneChip® Scanner 3000 7G System with AutoLoader

The scanner, operated through the GeneChip Operating Software, is used for data acquisition from expression and mapping arrays. It is equipped with a solid-state Green Laser and has a 16-bit data acquisition system. Specific features of this scanner include the use of the “flying objective technology”, an auto-zero sub-system and an auto-set laser power feature.

Quality control

Different pieces of equipment are commonly used on our platform to validate the quantity and quality of RNA and DNA samples.

Varioskan Flash Reader

This multimode reader from Thermo Scientific combines photometric and fluorometric detection technologies. It allows spectral analysis as well as measurements of any single wavelength in the UV/VIS/NIR range. It is commonly used for nucleic acid quantification. It is compatible with 96-well microplates as well as with the μDrop™ Plate, an accessory allowing the absorbance measurement of up to 16 microliter-scale samples (2 μl) simultaneously.

Qubit 2.0 Fluorometer

The Qubit®2.0 is a benchtop fluorometer for the quantitation of DNA, RNA, and protein, using the highly sensitive and accurate fluorescence-based Qubit™quantitation assays. The use of dyes selective for dsDNA, RNA, and protein minimizes the effects of contaminants on quantitation. Furthermore, performant illumination and detection technologies allow you to use as little as 1 μL of sample and still achieve high levels of accuracy, even with very dilute samples.

Agilent 2100 Bioanalyzer and AATI Fragment Analyzer

They both use microfluidic Lab-on-a-chip technology for the analysis of DNA, RNA and proteins as an alternative to standard gel electrophoresis techniques. They offer fast, reproducible and high quality digital data with minimal sample and reagent consumption. They are commonly used to facilitate the analysis of total RNA integrity or to validate the size or concentration of DNA sequencing libraries.

Sonicator

The covaris E220 AFA system is a focused ultrasonicator used for DNA and chromatin shearing. It applies focused acoustic energy to samples in closed tubes and in an isothermal environnement, preventing sample contamination and thermal degradation while providing highly reproducible results.This shearing technology generates tight DNA fragment distribution centered from 100 bp to 5 kb using as little as few ng of starting material.

Last update on Thu 16 Feb 2017

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