Next Generation Sequencing platform– Illumina HiSeq3000
The NGS platform includes a state-of-the art Illumina Hiseq3000 and is supported by a cBOT cluster station. The Illumina HiSeq3000 is a next-generation sequencing platform that uses a massively parallel sequencing- by-synthesis approach to generate billions of bases of high-quality DNA sequence per run. Applications include: DNA sequencing, gene regulation analysis, sequencing-based transcriptome analysis, SNP discovery and structural variation analysis, cytogenetic analysis, DNA-protein interaction analysis (ChIP-Seq), and sequencing-based methylation analysis. GenCore also houses other Illumina platforms namely, HiSeq1000, miseq and the automated library prep system- NeoPrep.
The Qiagen Qiacube is used to extract RNA or DNA at the GenCore. Qiacube offers seamless automation of the complete extraction process.
QC Suite: Thermo Nanodrop 2000, Agilent Bioanalyzer and 4200 Tapestation and Invitrogen Qubit
Thermo Nanodrop2000 spectrophotometer is used for UV spectrophotometric measurements to determine the RNA/DNA concentration and optical density (OD) 260/280 ratio. GenCore also used the Qubit and SpectraMax equipments for fluorescence based quantitative analysis of Nucleic acids
The Agilent 2100 Bioanalyzer performs capillary electrophoresis on minute quantities of RNA, DNA and protein samples and is used for sizing and quality assessment of Nucleic acids at the GenCore. The Bioanalyzer is considered the industry standard for assessing the quality of RNA based on its RNA integrity number (RIN) system.
The Qubit is used at the Gencore to quantitate nucleic acids and to quantitate libraries prepared for NGS. The Qubit fluorometer and SpectraMax employs specifically designed fluorometric technology using proprietary dyes to quantitate biomolecules of interest. These dyes are highly selective and very sensitive and emit signals only when bound to a specific biomolecule.