Victorian Centre for Functional Genomics

Our data analysis and machine learning platform is the cornerstone of the outputs generated from all the screens performed with us. Our key strength is in quantitative cellular phenotyping of cells grown in 2D and spheroids and organoids following perturbation in arrayed screening formats. We have developed sophisticated and highly customisable analysis pipelines by a team of specialised analysts, enabling us to assist you in interpreting the response of morphological perturbation in the cells using an unbiased method, dissect cellular responses and make therapeutic predictions (Choo et al 2021; Ramm et al 2022). 

For a more details, see our short explainer.

The Victorian Centre for Functional Genomics has established a high throughput pipeline for embedding cells or organoids in Matrigel using our robotic automation or customisable hydrogel using our Rastrum bioprinter instrument from Inventia Life Science. This platform enables highly complex co-culture interaction studies, including tumour and immune cells, host-pathogen interactions, angiogenesis and cell invasion. For a broader overview and some FAQs see our short explainer. 

Resources available: 

• Matrigel (sourced in large volumes to provide consistent lot numbers) 
• Hydrogel (Rastrum bioink)

With the Molecular Genomics Core we have recently developed a high throughput sequencing method called MAC-seq (Multiplexed Analysis of Cells). This can be performed in 384 well format in any experimental setting including time course analysis of growth or death, response to drug treatment and characterisation of patient materials in 3D matrices. Importantly, when coupled with high content imaging it allows us to perform 'Imaging Transcriptomics' further delineating our hit lists based on phenotypic quantitation together with target activity, see Li et al 2023. For a broader overview and some FAQs see our short explainer.

Using high throughput liquid handling automation, the Victorian Centre for Functional Genomics enables all types of compound screening approaches from cell-based to cell-free systems. We can deliver compounds in both 2D and 3D format and can accommodate dose curves with BYO drugs in multiple cell lines, 2- and 3-way drug synergy and large-scale collections. There is great creativity in this screening approach, and we work with you to develop the most appropriate experimental design and assay readouts. 

Resources available: 

• Accessed from Compounds Australia Griffith University (commonly screened libraries include the FDA, epigenetics, kinase inhibitor and scaffold collections, either as the whole collection or custom cherry picked) 
• BYO compounds welcome 

CRISPR screens enable researchers to determine resistance in their cellular model, facilitate biomarker discovery in patient samples or determine genes responsible for synthetic lethality. The Victorian Centre for Functional Genomics supports both synthetic and pooled CRISPR screening strategies. More details on this platform can be found below and in our short FAQ explainer.

Synthetic CRISPR

The synthetic CRISPR platform enables gene knockout in an arrayed format using liquid handling automation in 96- or 384-well format. This platform uses synthetic purified sgRNAs that are transiently delivered into Cas9-stable cells using lipid transfection reagents or nucleofected with purified Cas9 protein. The phenotype is assessed typically within 72-96 hours. This platform enables cell phenotyping approaches using high content imaging, fluorescence/luminescence plate reader end points or FACS profiling. 

Resources available: 

• Human whole genome arrayed sgRNA library (Horizon Discovery) 
• Screen as a whole genome (61 plates) or cherry pick custom sub-sets
• This library is part of a 3-way venture between the Victorian Centre for Functional Genomics, ANU Centre for Therapeutic Discovery and Functional Genomics South Australia and supported by Phenomics Australia
• Arrayed synthetic single crRNA kinome 
• Cas9 virus or protein 
• Nucleofection reagents 
• Purchasing sgRNAs at discounted rates

Viral CRISPR

The Victorian Centre for Functional Genomics houses both pooled and arrayed viral CRISPR libraries. Pooled CRISPR library are analysed using next generation sequencing. We take you through the screening process step-by-step for both whole genome pooled library or custom pooled sublibrary screens, from planning to execution through to analysis. The TransEDIT dual guide viral library in arrayed format can be used for single target validation, or boutique pooled library screening. 

Resources available: 

• CRISPR KO Brunello (human) and Brie (mouse) pooled libraries 
• CRISPRa Calabrese (human) and Caprano (mouse) pooled libraries 
• CRISPRi Docetto (human) and Dolomiti (mouse) pooled libraries 
• Custom pooled CRISPR sublibrary generation and reagents 
• Library amplification protocols and reagents 
• In-house NGS (in collaboration with Molecular Genomics Core) and analysis pipelines 
• Cas9 and dCas9 virus 
• TransEDIT dual guide whole genome human arrayed viral library

The end point assay of an arrayed screen can simply look at changes in cell viability following perturbation or can be far more complex with phenotypic outputs detecting changes at sub-cellular levels. Cell painting can be undertaken utilising any combination of validated cellular machinery stains and we have optimised staining protocols for both 2D adherent cells and 3D spheroid and organoid cultures. These phenotypic changes are then measured using our wide range of instrumentation that allows both live and fixed cell imaging in bright field and multi-channel fluorescence using either widefield or confocal microscopy. Collectively, we have a high throughput instruments that can maximise the amount of information we can obtain from any screen. 

Resources available: 

• Cell viability and Cell Painting dyes/antibodies

The siRNA platform is based on Horizon Discovery's siGENOME SMARTpool reagents arrayed in either 96- or 384-well plate format. siRNAs targeting the protein coding genome, miRNAs (mimic or inhibitor) or long non-coding RNAs are transiently introduced into cells using lipid-based reagents and assayed between 72-144 hours post-transfection. This platform offers similar readout options as screening arrayed CRISPR. 

The Victorian Centre for Functional Genomics has a pooled shRNA screening platform to enable stable knockdown in primary, non-dividing and standard cell lines. shRNAs can be screened singularly for validation purposes or screened as genome-wide or custom pools. The Victorian Centre for Functional Genomics together with the Molecular Genomics Core has developed the next-generation sequencing pipeline to identify the genes responsible for the biological phenotype of an assay.

• BioTek EL406: three units that aspirate and dispense media, cells, drugs and fix and stain 
• BioTek Multi-flo: like the EL406 but can aspirate and dispense any plate type and has a little more nozzle position control 
• Caliper ALH3000 liquid handling robot for all transfection and speciality liquid handling applications 
• Perkin Elmer Janus G3 liquid handling robot 
• Tecan D300E drug dispenser (excellent for BYO compounds, ultra-low dead volume, can randomise plate positions in a flash, super quick delivery)

• BioTek Cytation 5 plus BioSpa, a sophisticated plate imager and reader with live cell imaging 
• BioTek Cytation C10, a sophisticated imager with spinning disk confocal and plate reader 
• Fully automated Cellomics CX-7 LZR and CX-7 LZR Pro (2 units), laser light, wide field, confocal, live cell imaging
• Incucyte SX5 live cell imaging, metabolism module, wound healing x 2 instruments

• AMAXA 4D nucleofector and 96-well adaptor for high throughput
• Neon NxT electroporation system
• Barcode printer; all instruments are barcode-read enabled 
• EVOS Fl, bench top fluorescent microscope 
• IsoLight from Isoplexis 
• LiCONICs 220 stacking tower incubator 
• Rastrum 3D bioprinter 
• Seahorse metabolic bioanalyser