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 Graduate Medical School Singapore
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 and ABI 3730)
RNA Quantification (Agilent Bioanalyzer)
Publications and Testimonials

 

Microarray Expression and Methylation

 Affymetrix

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)

 

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. This assay provides quantitative methylation measurement at the single-CpG-site level, offering the highest resolution for understanding epigenetic changes. With the HumanMethylation27 BeadChip, researchers can quantitatively interrogate 27,578 CpG loci covering more than 14,000 genes at single-nucleotide resolution.

HumanMethylation27 assay 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 Unrestricted Human Microarray miRNA v14 Rev.2  expression profiling service is available.
(The array is based on Sanger miRbase release 14.0 update)

 

Sequencing (llumina Hiseq and AB 3730)

 Illumina Hiseq

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.

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

Full RNA-Seq service is available. (Multiplexing option available)

Sequencing service is available. (Multiplexing option available)

 

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.

 

Publications and Testimonials

 Publications

  1. Liang Goh, et al., Assessing Matched Normal and Tumor Pairs in Next-Generation Sequencing Studies, PLoS One.      2011; 6(3): e17810.
  2. J Tao, et al.,  CD44-SLC1A2 Gene Fusions in Gastric Cancer. Science Translational Medicine 2011 Apr 6; 3(77)ra30.
  3. Chia Huey Ooi, et al., Oncogenic Pathway Combinations Predict Clinical Prognosis in Gastric Cancer, PLoS Genet. 2009 October; 5(10): e1000676.
  4. Chia Huey Ooi, et al.,Oncogenic Pathway Combinations Predict Clinical Prognosis in Gastric Cancer. 2009 PLOS Genetics 5(10) doi:10.1371/journal.pgen.1000676.
  5. Kun Yu, et al.,A Precisely Regulated Gene Expression Cassette Potently Modulates Metastasis and Survival in Multiple Solid Cancers. 2008 PLoS Genetics. 4(7): e1000129.

 

Testimonials

  1. To the DGBF, I would like to thank you for providing timely service. This has significantly helped in advancing my research.  (Chan Kuan Rong, PhD student of NUS Graduate School program)
  2. I found the microarray service from the DBGF to be friendly, fast and reliable. The value was also the best out of all the places I checked before going with them. I hope to continue to work with them!  (Dr. Melissa Jane Fullwood, Duke-NUS Research Fellow)

 

For gifts-in-kind (shares, planned gifts, IT and lab equipment etc) or other any enquiries, please contact Mr. Dickson Lim at 6516 6696 or dickson.lim@duke-nus.edu.sg to discuss your gift.