Genomics/Equipment Park

The Genomics/Equipment Park STP provides access to state-of-the-art molecular biology instrumentation and offers instruction in the correct and efficient usage of the technologies involved. The range of equipment is constantly reviewed and specific requests from research laboratory heads are encouraged. The technologies and services include:

Service - DNA Sanger Sequencing -
Applied Biosystems 3730XL DNA Analyzer

Sanger Sequencing is provided as a service, with reaction set- and clean-up performed using liquid-handling systems. Reagents, sequencing protocols and trouble-shooting advice can be obtained from the facility staff.

Service - Plasmid DNA Extraction -
Qiagen BIOROBOT Universal

Automated medium- to high-throughput applications in a 96-well format. The system enables purification of nucleic acids from a variety of sample types. Currently purification of plasmid DNA from bacteria is offered as a service.

Service - RNA Extraction - QIAGEN QIACube

The system allows for automated sample preparation using QIAGEN spin columns. These include purification of RNA, genomic DNA, plasmid DNA, viral nucleic acids, and proteins, plus DNA and RNA clean up. Currently RNA purification on the system is offered as a service.

Real-Time PCR Quantification - Applied Biosystems
7900HT, 7500, ViiA7 Real-Time PCR Systems

The instruments are designed to detect fluorescence during the thermal cycling of polymerase chain reaction (PCR). By measuring the fluorescence intensity at each cycle, the system produces amplification plots that provide a more complete picture of the PCR.

Microarray Analysis - Affymetrix GeneChip Scanner

GeneChip expression arrays enable researchers to monitor genome-wide expression profiles. This global view helps in the understanding of the biological mechanisms of complex diseases and processes. Tiling arrays can be used to identify novel transcriptional elements and evaluate antisense transcription. GeneChip mapping arrays allow researchers to perform linkage analysis, association and copy number studies.

Shimadzu MultiNA

A microchip electrophoresis system for DNA/RNA analysis, providing an alternative to agarose gels. Applications include single or multi-plex PCR products, restriction digests and small plasmids (up to 2500bp).

The Beckman FX - liquid handling robot

A dual 'pod' automation system for parallel pipetting, and other liquid transfer techniques. Its low volume capability helps miniaturise reaction setups and save on costly reagents. The system has a stacker carousel which feeds micro-titre plates and tip-boxes into the system, allowing multi-plate transfers. A Span-8 configuration featuring independent well access is also available for tube-based operations and where flexible access to wells in a plate is needed.

Applications include:

  • High-density replication
  • Assay plate set-up (PCR, quantitative PCR (384 well), ELISA, kinase etc.
  • PCR and sequencing reaction clean-up using paramagnetic technology

The QIAgility

A bench-top instrument for automated setup of PCR reactions that is able to handle a wide variety of tube and plate formats. The system performs the preparation of master mix from individual reaction components and dilutions of standard series. Optionally available UV light and HEPA filter help to reduce the risk of sample carry-over.

PHERASTARPlus microplate reader

A premier multidetection HTS microplate reader with Simultaneous Dual Emission in all modes. The reader is able to perform all leading non-isotopic detection technologies including:

  • Fluorescence Intensity
  • Fluorescence Polarization
  • Time-Resolved Fluorescence
  • TR-FRET
  • Luminescence
  • Absorbance UV/Vis

Li-Cor Odyssey Infrared Imager

The imaging system offers a different way to analyse blots and gels. Odyssey is uniquely equipped with two infrared channels for direct fluorescence detection enabling simultaneous probing of two separate targets on the same gel, e.g. Western blots.

Beckman GenomeLab GeXP

The system employs a universal priming strategy for gene expression analysis by which up to 20 genes can be multiplexed in the same reaction.

Agilent 2100 Bioanalyzer - Service

The instrument detects biomolecules by laser-induced fluorescence. During chip preparation, a dye concentrate is mixed with the gel. With the help of the priming station, the channels of the chip are filled with the gel-dye mix. During the chip run, the dye intercalates directly with DNA or RNA. The system is used to quality control RNA before genomic analysis.

ImageQuant LAS 4000

A digital (CCD) imaging system for sensitive, quantitative imaging of gels and blots without film, by chemiluminescence and fluorescence. The high sensitivity and wide dynamic range is designed to capture the signals from ECL western blotting reagents. A wide range of visible fluorescent dyes can also be imaged via Red, Green and Blue epi-illumination (see Figure 1 below).

Figure 1

Figure 1. The knock-out of PTEN in MCF10A cell line does not change the levels of acetylation of Histone H3 Lysine 14. Total protein lysates from MCF10A parental Cell line (WT) and from the two independent clones of MCF10A Knock-out for PTEN (PTEN KO2 and PTEN KO3) were analysed by anti-PTEN, by ant acetyl-Histone H3 (Lysine 14) and by total Histone H3 antibodies. Anti-Vinculin antibody was employed as a loading control. Lysate from MCF10A WT cells treated with the Histone deacetylases inhibitor Trichostatin A (first lane) were used as a positive control for the acetylation of the Histone H3 Lysine14. Image courtesy of Davide Zecchin – Signal Transduction Group.

 

Graham Clark

Graham Clark (Lead) 

graham.clark@crick.ac.uk
+44 (0) 20 7269 3027