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). See our data analytics explainer for more details.

The VCFG 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)

Using high throughput liquid handling automation, the VCFG 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. VCFG supports both synthetic and pooled CRISPR screening strategies. More details on this platform can be found below and 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 VCFG, 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 VCFG 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