Victorian Centre for Functional Genomics at Peter Mac

Compounds

Accessed from Compounds Australia Griffith University. BYO compounds are welcome

Functional Genomics

Cell embedding in 3D matrices Drug synergy and interaction studies Live imaging High content imaging Technology development

Proteomics

Single cell proteomics using the Isoplexis Isolight BYO compounds welcome

Technology Development

The VCFG provides a complete screening service, which includes data analysis and it is here that we invest significant energy to ensure that we are updating our pipelines and innovating to maximise the outcomes and identify the most robust hit list. In particular, our focus is on ways to phenotype cells using high content imaging, and by extension, using machine learning strategies to identify target agent activity within screens and across multiple cell lines. We are currently developing ways to integrate phenotypic data with other multi-omics technologies. We have data analysis pipelines for drug and synthetic CRISPR screens in 2D adherent cells using imaging at any scale, single channel to complex multi-parametric staining. Within the 3D space, we can embed cell lines, PDX or PDO's in matrices using automation, which allows us to characterise growth, quantitate structure size, viability and response to death or morphology inducing agents. This is all built on bright field and fluorescent imaging methodologies. Recently we have developed high throughput transcriptomics in conjunction with the Molecular Genomics Core Facility at PeterMac. Using MAC-seq, sequencing can now be performed at scale, from cells cultured in 384 well format, allowing a transcriptional profile from cells treated with drugs, CRISPR or RNAi and or more simply, just characterising patient cells grown in 3D over time. We are developing the tools to integrate the phenotypic and genotypic outcomes of a screen. Nucleofection using single guide CRISPR, or multiple targets together can be performed and we have now developed methods to nucleofect in 96 well format, primarily for introduction of guide RNAs into suspension cells in a screen setting. Single cell proteomics using IsoPlexis, primary application in immune cell signalling.

Screening resources

Human whole genome arrayed sgRNA library (Horizon Discovery). 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. TransEDIT dual guide whole genome human arrayed viral library. Library amplification protocols and reagents. In-house NGS and analysis pipelines.

Bioinformatics and Data Analysis

Fully customised cell phenotyping pipelines for screens in 2D and 3D

Fully automated CellInsight CX7-PRO x 2 units and CX7-LZR, widefield, confocal, live-cell imaging up to 60x magnification. Cytation C10 spinning disk confocal, Cytation 5, widefield imaging

Incucyte SX5 (red, green, orange channels) Cytation 5 via the BioSpa incubator

Cytation 5 and C10 both are sophisticated plate readers that have spectral monochromators, direct injection for kinetic measurements, luminescence, fluorescence and alpha screen enabled

Caliper ALH3000 and Janus G3 liquid handling robots for all transfection and speciality liquid handling applications Rastrum 3D bioprinter for embedding cells in hydrogels BioTek 406: three units that aspirate and dispense media, cells, fix and stain BioTek multi-flo: aspirate and dispense any plate type Tecan D300E digital drug dispenser. Mini-Fontus for high throughput Legend-Plex staining.

AMAXA 4D nucleofector and 96 well adaptor for high throughput Seahorse metabolic bioanalyser LiCONICs 220 stacking tower incubator EVOS Fl, bench top fluorescent microscope Barcode printer; all instruments are barcode-read enabled Dedicated and fully backed up server for data and image storage