Blizard Institute - Barts and The London

Phenotypic Screening Facility

The phenotypic screening facility house all the equipment, software and support needed to facilitate a broad spectrum of screening project. Whether you would like to screen the whole genome or simply automate image acquisition, we have some of the most advance, fully automated systems available. The facility is open to all staff across QMUL and external users and is fully supported by dedicated staff.

The facility is in three main sections:

  1. Liquid handling robotics (Cybio) capable of si/sh/CRISPR or compound addition as well as automated cell seeding, medium changes, cell fixation and staining in 96 or 384 well formats.
  2. Automated high throughput image acquisition using fully versatile widefield (INCA2200) and confocal (INCA6000) imaging systems (GE)
  3. High content image analysis using dedicated software and analysis workstations (Developer Toolbox and INCarta (GE))

To date, the facility has successfully completed a number of high-content miRNA, genome-wide siRNA and compound screens (see Publications).

The imaging equipment within the facility also forms part of the AMIS umbrella which is a strategic investment to draw together state-of-the-art advanced molecular imaging equipment acorss QMUL. More information can be found here.

Facility Equipment

Liquid Handling

About

The Cybio is a liquid handling system that is full programmable allowing flexible assay development for screening projects.

Key Features

    • Works with 96 and 384 well plate
    • Stamp out compounds, si/shRNA and CRISPR libraries from master plates to daughter plates
    • Automated cell seeded through dropper system
    • Automated medium change
  • Automated fixation and staining protocols
  • Consistent results from plate 1 to plate 100
  • Operated by trained facility staff

 

 

 

 

Screening Libraries

About

As well as housing all the equipment required for your screen we also house a number of screening libraries ready to use.

Available Libraries

siRNA

  • Genome-wide siRNA library – Pools of 3 siRNAs from Ambion (251x 96 well plates or 63x 384 well plates)
  • Genome-wide siRNA library – Pools of 4 siRNAs from Qiagen

miRNA

  • miRNA library – 328 pre-miRNAs & anti miRNAs from Ambion
  • miRNA library – 837 miRNAs (Sanger V11) from Qiagen (12x 96 well plates in triplicate or 3x 384 well plates in triplicate)

Compound

FDA Approved oncology Drug Set VII –

https://wiki.nci.nih.gov/display/NCIDTPdata/Compound+Sets

INCA 2200 - Widefield System (LED)

About

The INCA 2200 is a super-fast full automated and sensitive wide-field imaging system. 

Key Features

  • Bright solid state and stable LED light source for standard four colour imaging as well as brightfield, Phase and DIC.
  • Stage supports slides and well plates from 6-well -> 1536-well and any plate type with a SBS footprint
  • Environmental control for live cell imaging
  • Liquid handling modules
  • On-the-fly deconvolution software
  • Capable of 3D imaging and max intensity projection
  • Smart review scanning feature allow automated reimaging of hits.
  • Integrated with robotic arm for 24hour plate loading

 

INCA 6000 – Confocal system (Laser)

About

The INCA6000 is a laser based automated confocal instrument that has a fully adjustable aperture to match your imaging needs

Key Features

  • Four lasers (405, 488, 561 and 642 nm)
  • Stage supports slides and well plates from 6-well -> 1536-well and any plate type with a SBS footprint
  • Environmental Control for live cell imaging
  • Liquid handling modules
  • Preview, count on the fly, 3D imaging, Max projection, Smart review scanning feature (NEW)
  • Unlike conventional confocal imaging systems that are often stuck with a set pin hole, the INCA6000 has a adjustable aperture which can be set on a per channel bases. This allows a user to decide on the level of confocality required.

 

High content software

About

Manual nuclei counting or measuring the area covered by foci with programs like ImageJ can be incredibly tedious and time consuming. Fully definable high content analysis software removes this bottleneck allow for bespoke protocols to be written that will give you phenotypic data on a per object (foci, nuclei, cell), per field and per well bases. Once written the protocol can be set to run and report back the data with a simple excel file.

Key Features

  • Licences for both Developer ToolBox (GE) and the new INCarta (GE) software
  • Flexible assay development
  • Unbiased data analysis
  • Loading of images not taken with facility equipment possible
  • Four high spec workstation analysis machines
  • Cutting edge analysis algorithms for cell segmentation
  • Continuous training and support for users available 

Data Storage

About

Data storage is often an afterthought when applying for grants and planning a screen. High throughput instruments can take an incredible number of high quality images very quickly. Combine this with 3D imaging, time series or large scale screen projects and you will generate several TBs of data. Within the screening facility we house our own data storage to accommodate even the largest of projects.

Key Features

  • Up to 60TB of available storage
  • Images saved directly to core facility storage to stop any bottleneck in image acquisition
  • Networked servers allowing immediate access to files from analysis machines
  • RAID6 data protection with automatic hot swapping drives in case of disk failure.
  • Nightly backup to secondary site for disaster proofing of your precious data

 

Seahorse XF24

About

With the ability to measure real-time oxygen consumption rate (OCR) and the extracellular acidification rate (ECAR) the Seahorse allows metabolic screening of your cultures

Key Features

  • 24 well analysed at once
  • Programmable screening protocol for tailoring to your assay needs.
  • Available kits include: Glycolytic rate, Mito Stress, Energy phenotype and Mito fuel kit

Luke Gammon (Facility Manager)

e-mail: l.gammon@qmul.ac.uk

Mobile: 07985337721

Desk: 0207882 2342

Screening Room: 0207882 2404

 

Cleo Bishop (Academic Lead)

e-mail: c.l.bishop@qmul.ac.uk

For training or booking please contact facility manager (Luke Gammon) or by using the iLabs Booking system https://qmul.corefacilities.org/service_center/show_external/3579

Equipment Internal (p/H) External (p/H) Internal (O/N 5pm-9am)  External (O/N 5pm-9am) 
INCA2200 £24 £60 £100 £200
INCA6000  £24 £60 £100 £200
Analysis (Developer)  Free  Please contact core manager  Free  Please contact core manager 
Analysis (INCarta)  Free  Please contact core manager  Free  Please contact core manager 
Cybio Liquid Handling System  Please contact core manager  Please contact core manager  Please contact core manager  Please contact core manager 
Screening Libraries  Please contact core manager  Please contact core manager  Please contact core manager  Please contact core manager 
Seahorse  Free  Please contact core manager  Free  Please contact core manager 

Please contact us to discuss charges for extended imaging times such as large scale screening projects or long-term live cell imaging

 

Selected Publications

  • Biddle, A. et al., 2016. Phenotypic Plasticity Determines Cancer Stem Cell Therapeutic Resistance in Oral Squamous Cell Carcinoma. EBioMedicine, pp.1–8. Available at: http://linkinghub.elsevier.com/retrieve/pii/S2352396416300056.
  • Lewis, A. et al., 2015. Low Serum Levels of MicroRNA-19 Are Associated with a Stricturing Crohn’s Disease Phenotype. Inflamm Bowel Dis, 21(8), pp.1926–1934.
  • Lowe, R. et al., 2015. The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans. Genome biology, 16, p.194. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4574115&tool=pmcentrez&rendertype=abstract.
  • Murray, A. et al., 2015. Brief report: Isogenic induced pluripotent stem cell lines from an adult with mosaic down syndrome model accelerated neuronal ageing and neurodegeneration. Stem Cells, 33(6), pp.2077–2084.
  • Overhoff, M.G. et al., 2014. Cellular senescence mediated by p16INK4A-coupled miRNA pathways. Nucleic Acids Research, 42(3), pp.1606–1618.
  • Nijhuis, A. et al., 2014. In Crohn’s disease fibrosis-reduced expression of the miR-29 family enhances collagen expression in intestinal fibroblasts. Clinical Science, 127(5), pp.341–350. Available at: http://clinsci.org/lookup/doi/10.1042/CS20140048.
  • Liu, L. et al., 2011. A whole genome screen for HIV restriction factors. Retrovirology, 8(1), p.94. Available at: http://dx.doi.org/10.1186/1742-4690-8-94.
  • Borgdorff, V. et al., 2010. Multiple microRNAs rescue from Ras-induced senescence by inhibiting p21(Waf1/Cip1). Oncogene, 29(15), pp.2262–2271. Available at: http://dx.doi.org/10.1038/onc.2009.497.
  • Bishop, C.L. et al., 2010. Primary cilium-dependent and -independent hedgehog signaling inhibits p16INK4A. Molecular Cell, 40(4), pp.533–547. Available at: http://dx.doi.org/10.1016/j.molcel.2010.10.027.

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Blizard Building

Queen Mary's University of London

4 Newark Street

London E1 2AT