Duke-NUS Genome Biology Facility

Duke-NUS Genome Biology Facility (DGBF) was set up in 2008 by Duke-NUS to cater to the needs of researchers who are interested in using high end genomics technology such as microarray and sequencing.

We are constantly upgrading to newer technology such as Next-Generation Sequencing (NGS) to provide our customers with more flexibility to choose the technology that best suits their projects.

In DGBF, we aim to facilitate biomedical research through genomic technology and we strive to provide our customers with professional advice and reliable results within the shortest time.

Please contact us at:
Duke-NUS Medical School
8 College Road Singapore 169857
Phone: +65 6516 1924/ +65 6516 1945
Email: genomics@duke-nus.edu.sg

Microarray Expression and Methylation
Sequencing (illumina Hi-Seq 2000 and ABI 3730)
RNA Quantification (Agilent Bioanalyzer)
Publications and Testimonials 

Microarray Expression and Methylation

 Affymetrix

GeneChip® Human Genome U133 Plus 2.0 Array:

The Affymetrix GeneChip® 3' expression arrays interrogate each gene with multiple independent probes, offering an accurate, robust and reproducible 3'-based, gene-level expression profiling. This system allows the flexibility to view the genome at a global level or focus on a specific subset of genes.

Human Genome U133 Plus 2.0 array : analyzes the relative expression level of more than 47,000 transcripts and 
variants.

Human Genome U133 Plus 2.0 array and Gene Chip Mouse Genome 430 2.0 array expression profiling services are available
(Each sample to be hybridized to each array)

GeneChip® PrimeView™ Human Gene Expression Array:

The latest product by Affymetrix that enables researchers to measure gene expression of more than 36,000 transcripts and variants (>20,000 genes). Sequences used in the array design covers all well- annotated genes and transcripts from RefSeq version 36. Sequences were also selected from the UniGene database 219 and full-length human mRNAs from GenBank®.

*Newly added service: GeneChip PrimeView Human Gene Expression Array profiling service is available

GeneChip® Human Gene 2.0 ST Array:

This array offers whole- transcript coverage by interrogating > 30,000 coding transcripts and >11,000 long intergenic non-coding transcripts. It allows the study of whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events.

*Newly added service: GeneChip Human Gene 2.0 and 1.0 ST Array expression profiling services are available

 Illumina 

Gene Expression 

The Illumina® Whole-Genome Gene Expression Direct Hybridization Assay offers the highest level of multiplexing for whole-genome expression profiling available .  For Human With the most up-to-date expression content and high-throughput processing, Illumina's whole-genome expression arrays produce high-quality data for large gene expression studies, efficiently and economically. The HumanHT-12 v4 Expression BeadChip is Illumina's latest whole-genome expression array, providing coverage for more than 47,000 transcripts and known splice variants across the human transcriptome. Human HT-12 v4 allows researchers to profile 12 samples on each array.

HumanHT-12 v4 and MouseWG-6 v2 Expression profiling services are available

Infinium Methylation

DNA methylation plays a critical role in the regulation of gene expression and is known to be an essential mechanism for guiding normal cellular development and maintaining tissue identities. Numerous studies have implicated aberrant methylation in the etiology of many human diseases including cancer. The Infinium Methylation Assay is based on genotyping bisulfite-converted genomic DNA and it provides an efficient solution for surveying genome-wide DNA methylation profiles across samples. The Infinium HumanMethylation450 BeadChip allows interrogation of more than 485,000 methylation sites per sample at single-nucleotide resolution and higher sample throughput.

 Infinium HumanMethylation450 BeadChip profiling service is available 

Agilent MicroRNA (miRNA) Expression

Studies have shown that distinct miRNA expression patterns are associated with a number of tumor types as well as involved in regulating processes such as cell development, metabolism and viral infections. Because miRNAs are potential regulators of gene expression, scientists are increasingly interested in measuring them for research, drug discovery, other therapeutics and as diagnostic tests. Agilent microRNA platform allows the generation of comprehensive miRNA expression profiling.  This assay requires low total RNA sample input, includes a straightforward and easy procedure  for labeling and detection. 

Agilent Human MicroArray miRNA v19 expression profiling service is available.

(The array is based on Sanger miRbase release 19.0 update) – 2006 human miRNAs represented on the array. 

Sequencing (Illumina Hiseq 2000 and ABI 3730)

 Illumina Hiseq 2000

Illumina HiSeq is a next-generation sequencing platform which employs illumina’s reversible terminator-based sequencing by synthesis chemistry. It enables massively parallel sequencing of millions of fragments with high accuracy that eliminates sequence-context specific errors, enabling robust base calling across the genome, including repetitive sequence regions and within homopolymers.

Hi-Seq equipment was acquired using a grant from the Cancer Science Institute of Singapore.

It is capable of generating up to 160Gb per run for a total of 8 lanes with 2 x 76bp read length (based on in-house data). The ability to specify read length, single read or paired end reads, and multiplexing of up to 24 samples per lane allows specific tailoring to suit any project.

RNA

 RNA Sequencing allows analysis of novel transcripts, novel isoforms, alternative splice sites, rare transcripts, and cSNPs. illumina’s TruSeq RNA sample preparation kit produces a poly-A enriched cDNA library. rRNA depleted RNA-Seq allows for capture of both mRNA and multiple forms of non-coding RNA.

 Full RNA-Sequencing service is available (multiplexing option available)

*Newly Added service: rRNA depleted RNA-Sequencing service is available (multiplexing option available) 

DNA

 DNA sequencing of DNA libraries for whole-genome resequencing can be carried out using illumina’s TruSeq DNA Sample preparation kit. Exome Sequencing can be carried out using Agilent SureSelect all Exon kit (either v4 or v5 kit).  

Full Whole-genome Sequencing service is available (multiplexing option available)

*Newly Added Service: Full Exome-Sequencing service is available (multiplexing option available)

Partial service: Hi-Seq Sequencing service is available (customer to provide constructed libraries)

Applied BioSystems Sanger Sequencing for ready to run pellets

The Applied Biosystems 3730 DNA Analyzer is an automated, high throughput, capillary electrophoresis system used for analyzing fluorescently labeled DNA fragments. It combines reliability, high data quality, and production capacity to provide the ideal platform for rapid and accurate DNA analysis.

DNA sequencing service (on ready to run pellets) available.

This service requires the user  to set up their own sequencing reactions and also purification.  The user will bring the samples to the facility in pellet format. SOP is available  to help  users to carry out the sequencing reactions and purification step in their laboratories. 

RNA Quantification (Agilent Bioanalyzer)

 Agilent Bioanalyzer

The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells. Results are delivered rapidly, in automated and high quality digital data. Miniaturization of analytical instrumentation has many advantages over conventional techniques. These advantages include improved data precision and reproducibility, short analysis times, minimal sample consumption, improved automation and integration of complex workflows.

Total RNA quality assessment service is available. 

Arcturus XT Laser Capture Micro-dissection

Laser Capture Micro-dissection (LCM) is a technique to isolate desired cell populations or tissues from a heterogeneous mixture of all other tissue components such as epithelia, stroma, blood vessels, etc. under microscopic visualization. ArcturusXT LCM is a unique system employing infrared and ultraviolet laser capture which enables the preservation of the integrity of captured cells without any change in morphology or biological content. The system removes the constraints of sampling bias by isolating pure populations of cells in an efficient manner, allowing isolation of nucleic acids for other downstream applications such as Next-Generation Sequencing, NanoString or PCR.  

Publications and Testimonials

Publications
Testimonials