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.

 

 

 

 

Publications and Testimonials

 

 Publications

  1. Zang Z.J., et al., Exome Sequencing of Gastric Adenocarcinoma Reveals Recurrent Somatic Mutations in Cell Adhesion and Chromatin Remodeling Genes. Nature Genetics. 44(5):570-574 (2012)
  2. Ivanova T., et al., An Integrated Epigenomic Screen Identifies BMP4 as a Modulator of Cisplatin Sensitivity in Gastric Cancer. Gut. 62:22-33 (2013)
  3. Zouridis H., et al., Methylation Subtypes and Large Scale Epigenetic Alterations in Gastric Cancer. Science Translational Medicine. 4(156):156ra140 (2012)
  4. Tan I.B., et al., Intrinsic Subtypes of Gastric Cancer, Based on Gene Expression Pattern, Predict Survival and Respond Differently to Chemotherapy. Gastroenterology. 141(2):476-485 (2011)
  5. Zang Z.J., et al., Genetic Structural Variation in the Gastric Cancer Kinome Revealed through Targeted Deep Sequencing. Cancer Res. 71(1):29-39 (2011)
  6. Tao J., et al., CD44-SLC1A2 Gene Fusions in Gastric Cancer. Science Translational Medicine. 3(77):77ra30 (2011)

 

Testimonials

 

  1. I am impressed with the fast and friendly response from both the technical and administrative staff. The lead time to completion of sequencing is pleasantly short.  [HiSeq WGS Sequencing] (Dr. Ng Sock Hoon, Research Scientist, DSO National Laboratories)
  2. We engaged DUKE-NUS Genomics Biology Facility to perform paired end sequencing for our mouse samples.  The turnover time is pretty fast from cDNA library submission to receiving the fast-q files. For each lane, we obtained more than 130 million reads. The quality of reads is quite good and about 70% reads can be mapped to the genome. [HiSeq RNA Sequencing] (Dr. Sun Lei, Assistant Professor, Duke-NUS Graduate Medical School)
  3. From initial sample preparation to the delivery of quality reads, DGBF provides excellent service at every step of the process and all at a very competitive price. [HiSeq RNA Sequencing] (Dr. October Sessions, Research Fellow, Duke-NUS Graduate Medical School)
  4. 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! [illumina Gene Expression] (Dr. Melissa Jane Fullwood, Yale-NUS Assistant Professor, Cancer Science Institute of Singapore Special Fellow)
  5. I have worked with different providers in the United States, my experience with DGBF is the best -superlative service. [illumina Gene Expression] (Dr. Lee Tih-Shih, Duke University Medical School, Durham, NC, Duke-NUS Graduate Medical School Associate Professor)
  6. We did our gene expression profiling with DGBF, and we are very impressed and satisfied with their service. They are approachable, efficient, professional and attentive to customer’s needs. In addition, they do proper quality checks on samples before running the arrays, and they provide reliable results. [illumina Gene Expression] (WayChamp, PhD student at NUS Graduate School program)
  7. The service of DGBF is very user-friendly. More importantly, the data they produce is consistent and of high quality. [Affymetrix Gene Expression] (Dr. Huang DaChuan, Research Fellow, National Cancer Centre)
  8. The Affymetrix expression profiling service provided is efficient, convenient and reliable. With just 600ng of sample required as compared to 30ug as requested by other vendors, precious samples can be profiled here. In addition, RNA quality is assessed before expression profiling is carried out and this provides researchers with the confidence that high-quality results are generated. With the quick turn-around time and reliability of the service rendered so far, I would highly recommend this to other users. [Affymetrix Gene Expression] (Bernice Wong, Research Officer, National Cancer Centre)
  9. We sent 50 samples to DGBF for Affymetrix U133 Plus arrays expression profiling and were very satisfied with the results. The data generation was fast after sending in our RNA samples and we have been impressed with the data quality and the service provided by DGBF. I would highly recommend this service for any researcher who is looking to obtain high quality gene expression data to accelerate breakthroughs in their research. [Affymetrix Gene Expression] (Dr. Tang Yew Chung, Research Fellow, Duke-NUS Graduate Medical School)