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Technologies

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The GenomEast 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

Illumina 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.

Illumina 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 microfluidics

Fluidigm Biomark HD System

biomark_large.gif The Biomark HD system is a high-throughput real-time PCR instrument 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.

Fluidigm C1™ Single-Cell Auto Prep System

The C1™ system provides an easy and reproducible platform to capture and process 96 or 800 individual cells for subsequent RNA or DNA analysis.

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 4000 using RNA-Seq technology for whole transcriptome analysis.

10X Genomics Chromium Controller

The Chromium Controller uses the 10X GemCode technology to encapsulate individual cells or genomic DNA into hundreds to tens of thousands of uniquely addressable partitions in minutes, each containing an identifying barcode for downstream analysis.

This system supports a growing number of single cell applications such as gene expression, CNV, or ATAC analyses. In addition, using the linked-reads technology, the Chromium can be used to generate long-range genomic data from Illumina short-read sequencing data with applications for exome or genome re-sequencing or de novo assembly.

 

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 Tue 19 Feb 2019

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