The ARC Biotechnology Platform

Located on the Agricultural Research Council’s Onderstepoort Veterinary Research campus, the Biotechnology Platform (ARC-BTP) was established in 2010 as a major strategic priority of the ARC. The role of the ARC-BTP is to create the high-throughput resources and technologies required for applications in genomics, quantitative genetics, marker assisted breeding and bioinformatics within the agricultural sector. The focus of the ARC-BTP is to establish itself as both a research and service driven institution, providing an environment in which highly skilled researchers can be hosted and trained. The technologies established within the platform are accessible as services to the ARC, collaborators, companies, science councils and researchers across the continent.

 

The ARC-BTP has implemented high-throughput DNA and RNA sequencing and genotyping technologies within the platform, with the capacity to genotype thousands of samples, or generates large volumes of data from single samples.

The current technologies available in the platform include:

  • Next generation sequencing and genotyping platforms
  • Liquid handling robotics systems
  • Laser capture micro-dissection microscope​

 

Next Generation Sequencing services 

The ARC-BTP operates three next generation Illumina sequencers, a HiSeq2500 and two MiSeq systems. Different sample preparation protocols are available for NGS library preparations, depending on the type of samples and/or the application. This is an area that gets regularly updated and the facility keeps abreast with these. The best approach with the current available technologies will be determined during initial discussion with clients.

 

Applications:

  • Whole genome DNA sequencing
  • 16S rRNA amplicon sequencing
  • Whole genome DNA re-sequencing
  • RNA sequencing

 

 

 

 

 

RNA Sequencing Services:

RNA-seq allows researchers to detect both known and novel features in a single assays, enabling the detection of gene fusions, single nucleotide variants and allele-specific gene expression without requiring prior knowledge.

RNA-seq is the gold standard for mapping transcriptomes, profiling changes in splicing and measuring gene expression levels.

Applications:

  • High throughtput (RNAtag) sequencing
  • mRNA and small RNA sequencing
  • Total RNA (Ribozero) sequencing
  • Ultra low input RNA sequencing

 

 

 

 

 

SNP Genotyping Services 

Genotyping enables the measurement of genetic variation between members of a species on the basis of single nucleotide polymorphisms (SNPs). Illumina BeadChips have been developed in collaboration with leading agricultural researchers. This means the SNP technology has been tried and tested by numerous agricultural organizations, industry and academia.

Application:

  • Copy Number Variation analyses

    Image courtesy of Illumina Inc.

  • Biobank sample analyses
  • Parentage analyses
  • Plant, Animal and Human screening panels
  • Targeted disease or rare variant panels
  • QTLs, GWAS, SNP discovery and forensics

 

 

 

SNP genotyping is performed using the Infinium bead chip technology of Illumina (plants, animals and human). Both commercial and custom made Infinium bead chips, ranging from 1000 up to more than a± 3 K-1 million,000 K SNPs, are available from Illumina (www.illumina.com). We recommend that clients contact us for ordering and pricing of these, since reagents have expiry dates and we need to schedule the work around these dates.

Image courtesy of Illumina Inc.

 

High throughput nucleic acid extraction 

The Hamilton star Plus is used for high throughput DNA extractions that. uses the Magnetic Bead Technology, it allows highly efficient nucleic acid isolation from a variety of samples at any throughput.

Key features:

  • High throughput  
  • No cross contamination
  • Multiple sample types
  • Adjustable protocols

 

 

 

Focused Ultrasonificator for Sample Preparation

The Covaris focused-ultrasonicator uses the acoustic technology: Adaptive Focused Acoustics™ (AFA), that mechanically shears the sample by applying very high frequency ultrasound waves or acoustic bursts. The shearing process is un-biased from temperature, sample GC content or concentration. It is able to produce consistent shearing of fragments ranging in size from 150 bp to 5 kb, for between one and ninety-six samples.

 

Applications of the COVARIS E220:

  • DNA/RNA shearing
  • Biomarker extraction
  • FFPE Nucleic acid extraction
  • Epigenomics
  • RNA-seq
  • Cell lysis

 

 

 

Laser Capture Micro-Dissection Microscope (LCM)

A highly specific specimen can be isolated with the focused laser of the PALM MicroBeam LCM and transferred to a collection tube. This allows researchers to separate their desired specimen from a population of cells or tissues at an early stage of their research work.  The system is ideal for single-cell isolation for use in downstream applications as cells remain viable.

Applications of the PALM MicroBeam Microscope (Zeiss):

  • Sample manipulation at microscopic scale
  • Highly specific cell and feature selection
  • Contamination-free isolation
  • Contact-free isolation

 

 

 

 

Technology under development: 

Optical Mapping

Use the Irys to produce fingerprints of large DNA molecules for the construction of genome wide maps. The Irys is able to directly image intact and labelled genomic DNA to enable high-resolution detection of structural variations in both plants and animal genomes. This technology is particularly useful for species with large repetitive regions.

Applications of the Bionano Irys:

  • Whole genome mapping
  • Structural variation detection
  • Sequence assembly
  • Sequence scaffolding

 

 

 

 

 

Real-time sequencing with ultra-long reads

The Oxford Nanopore technology has made the sequencing of ultra-long reads possible. Each MinION consists of 512 nanopore channels that are able to generate 5kb to 20kb or longer reads in real-time. Read lengths are determined by sample preparation, and is now approaching 1 Mb for a single read. This has particular benefits when assembling large, complex genomes, resolving structural variation or wishing to explore large metagenomic communities.

Applications of the ONT MinION:

  • Sequence assembly
  • Sequence scaffolding
  • Direct DNA or RNA sequencing

 

 

 

 

 

 

 

Contact Information:

General enquiry about ARC BTP Core Facility/Service:

Email:  

Phone: Phone: +27 12 529 9483

 

Dr Farai Muchadeyi

Senior Manager ARC Biotechnology Platform

Phone: +27 12 529 9352

Email: 

 

Lerato Mpye

Project Co-coordinator ARC Biotechnology Platform

Phone: + 27 79 506 8617

Email: 

 

Dr Dirk Swanevelder

Senior Researcher ARC Biotechnology Platform

Phone: +27 12 529 9472

Email: 

 

Dr Magriet Van Der Nest 

Senior Researcher ARC Biotechnology Platform

Phone: +27 12 529 9472

Email:

 

Dr Nokuthula Mchunu

Senior Researcher ARC Biotechnology Platform

Phone: +27 12 529 9356

Email:

 

Dr Rian Pierneef

Researcher ARC Biotechnology Platform

Phone: +27 12 529 9356

Email: 

 

Location

The ARC BTP is housed on the ARC Onderstepoort Campus

Agricultural Research Council

Onderstepoort Campus

100 Old Soutpan Road (M35)

Biotechnology Platform Building (Building 38)

GPS co-ordinates:

25°39’03.10″S

28°11’03.10″E