Sullivan Lab

@SAiGENCI are proud to announce @LukeIsbel as @UniofAdelaide first Viertel Fellow. Find all the details at bit.ly/4e1NeKi Congratulations Luke! Excited to see the next stage of your science develop here at @SAiGENCI! @ACEpigenetics 👏🎉🧪

ACE is honoured to celebrate Dr Qi Zhang's prestigious @CSL Centenary Fellowship! What an incredible achievement. Congratulations @QiZhang85, we cannot wait to see what's next 🧬👏 @EMBLAustralia @UniofAdelaide @SAiGENCI

Following several kind requests, here is a high-level summary of our pre-print in @biorxivpreprint (doi: doi.org/10.1101/2024.1…): STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging STAMP is a scalable, cost-efficient method for single-cell transcriptomics and multimodal profiling through imaging. It bypasses sequencing, significantly reducing costs while enhancing throughput. #SingleCellRNA #SpatialOmics #STAMP The motivation for this paper comes from the limitations of current scRNA-seq methods, which are costly, inefficient, and struggle to capture low- and high-abundance transcripts. Challenges like droplet instability, cell damage, limited cell capture, cross-contamination, inefficient indexing, and high sequencing costs affect ultra-low and ultra-high cell profiling, hindering accurate analysis of complex cell populations. #Limitations #DropletMicrofluidics STAMP addresses these issues with a scalable, cost-effective, sequencing(costs)-free approach that works efficiently across ultra-low to ultra-high cell numbers, while preserving cellular morphology and enabling multimodal profiling. #SpatialOmics #UltraLow #UltraHigh STAMP uses an imaging-based approach to perform high-throughput RNA and protein profiling by stamping cells onto slides compatible with CosMx and Xenium platforms, allowing multimodal profiling in a single run. #Proteomics STAMP supports single-modal (RNA/protein) and multimodal (RNA + protein) profiling, enhancing experimental flexibility and scalability. This versatility is essential for large-scale atlases and mixed-sample experiments. #SingleCellAtlas #MultiSampleProfiling STAMP scales easily: from less than 100 to millions of cells. It overcomes limitations in droplet-based systems, where throughput is often constrained by sequencing costs. #HighThroughput STAMP handles diverse sample types: PBMCs, dissociated tumors, nuclei, and stem cells. It also excels with fragile or archived tissues, where traditional methods often fail to yield high-quality data. #ArchivedSamples STAMP eliminates sequencing costs, making large-scale single-cell analysis accessible to more labs. #CostEfficiency Here’s a cost comparison between GEM-X and STAMP-X for RNA profiling: GEM-X RNA (20k cells): $0.0764/cell 1M cells = $76,400 (cost/cell = $0.0764) 2M cells = $152.800 (cost/cell = $0.0764) 3M cells = $229,200 (cost/cell = $0.0764) STAMP-X RNA (1M cells): $0.0075/cell 1M cells = $7,500 (cost/cell = $0.0075) 2M cells = $7,500 (cost/cell = $0.00375) 3M cells = $7,500 (cost/cell = $0.0025) In STAMP cells remain intact after imaging, enabling further downstream applications like histological validation or additional molecular assays, adding value to each sample. #NonDestructiveAnalysis We tested STAMP’s sensitivity by identifying, ultra-rare, circulating tumor cells (CTCs) spiked into PBMCs at 1:100,000. Such sensitivity is essential for clinical diagnostics, particularly in rare cell detection. #CTCs #CancerDiagnostics In a high-throughput immuno-phenotyping experiment, STAMP profiled 1.7M PBMCs, capturing a median of 83 transcripts and 49 genes per cell. This resulted in high-resolution immune profiling. #Immunology #HighThroughputProfiling 31 immune cell states were mapped in PBMCs, capturing rare subpopulations (Th1/Th2/Th17 and NK subtypes). Detailed immune phenotyping is critical for understanding immune diversity in health and disease. #ImmuneMapping Whole cells vs. nuclei: STAMP's ability to profile both whole cells and nuclei is crucial for samples with low RNA content (e.g., archived tissues), increasing the platform’s applicability. #NucleiProfiling #SingleCellOmics STAMP integrates RNA and protein profiling. In cancer cell line profiling, RNA and protein data showed strong correlations, confirming the platform’s robustness in multimodal data collection. #MultimodalProfiling STAMP’s multimodal profiling produced high-resolution immune maps, combining RNA and protein data. This approach is essential for dissecting complex immune states and understanding functional responses. STAMP excels in low-input samples. We demonstrated its ability to accurately profile as few as 100 cells, which is critical for studying rare populations in small samples. #LowInput #RareCell In a BMP4-driven stem cell differentiation model, STAMP captured dynamic changes from pluripotency to mesoderm and endoderm progenitors over multiple timepoints, tracking lineage differentiation. #StemCellDifferentiation #LineageTracing Trajectory analysis shows that STAMP’s resolution makes it a powerful tool for developmental biology and perturbation studies. #DevelopmentalBiology #hESC STAMP allows multi-sample profiling on a single slide, reducing batch effects and improving comparative analysis, particularly in drug response and perturbation studies. #MultiSampleAnalysis #PerturbationScreening STAMP represents a significant advance in single-cell research, offering scalable, multimodal RNA/protein profiling at low cost. Its versatility will support a broad range of research, from basic to clinical. #SingleCellTechnology Lots more coming soon... @DrJasPlummer @hoheyn @pascual_reguant @EmanuelePitino1 @helucro @ximbaozao @irepan_salvador @Kellieiswise @m_mohenska @jc_nietos @cnag_eu @StJudeResearch @ACEpigenetics @M_ayco_N @eliseinsing Bill Flynn, Yutian Liu, Hannah Chasteen

Pretty stoked to win an ASBMB poster prize at @bmh2024Melb, alongside fellow eye CRISPR PhD candidate and friend Lachi Staker 🧬✂️👀

ICYMI: we are hiring! Come and join us ⁦@MRC_LMS⁩ for a #postdoc #regulatorylogic #devbio #stemcellmodels in an excellent environment with fantastic support and colleagues :) thenode.biologists.com/jobs/postdoc-i…

Don’t miss out on discounted rates for the ASSCR ASM! Register by 27th Sept to secure your spot 👉 asscrmeeting.com.au/registration Reminder: Book your flights & accommodation early to avoid high costs. ✈️🏨 See you in Adelaide!

📢🎉 Our lab is recruiting x3! #Postdoc & #PhD Join from🌏 inc AU, EU, US! Great scientific environment and a very attractive salary. 1. #AI for #singlecell biology 2. #Multiomics, immuno diagnosis (sc+spatial+metab.) 3. #tidyomics + #HPC Plz share! 🙏mangiolalaboratory.github.io/Mangiola-Lab-O…

Professor Jose Polo FAA (@UniOfAdelaide), a leading biochemist, stem cell biologist and now Academy Fellow, has significantly advanced our knowledge of cellular reprogramming—the process by which cells transform into different types. His innovative work combines cellular models, genomics, and computational methods, propelling forward the fields of reprogramming and stem cell research. Polo's influential work has had a global impact, fostering scientific progress and industrial applications. #FellowsAA

Congratulations to ACE leaders Jose, @SullivanLab8 and @LukeIsbel for their outstanding presentations and work on cancer epigenetics at @SAiGENCI ‘s second annual public lecture! (Video link @ the end) (1/5)

Loving #Visium HD! 32 scheduled runs non-stop till October, plus ongoing #Chromium and #Xenium projects! We need help…tons of it!. Living in Australia and interested in a paid internship? Then email me or my team directly, and we can discuss the details. It can be fun!