Dreamcatcher allows accurate identification and quantification of bacterial reads in single-cell, spatial, and bulk RNA-seq

- Microbial reads are often discovered in RNA-seq samples; however, accurate identification of relevant bacteria is very challenging.

- We have developed a pipeline that allows us to remove computational false positives, evaluate "contaminome" contribution, and analyze single cell/spatial reads together with the host data.

- We will present a tutorial on performing this analysis and the types of biological information that can be learned from our approach.

Computational analyses of single-cell: technology landscape and its best practices

- Dreamcatcher allows accurate identification and quantification of bacterial reads in single cell, spatial, and bulk RNA-seq.

- Discuss different possibilities enabled by technology using single-cell. Discuss the best practices in choosing the right pipeline for an analysis.

- A workshop of developing small pipeline for an analysis.

Integrating single cell and spatial transcriptomics to uncover novel immune functions of adipocytes to parasitic infection

- Trypanosoma brucei is an extracellular parasite that causes adipose tissue wasting and weight loss, and poses a massive risk to the health of people living in Sub-Saharan countries in Africa

- By integrating single cell and spatial transcriptomics of the skin and subcutaneous adipose tissue, we uncovered novel interactions between adipocytes and IL-17A+ immune cells, such as gdT cells, that may lead to adipose tissue wasting

- Our integrated analyses also led us to identify that adipocyte IL-17 signalling is important for controlling local parasite number, demonstrating that adipocytes form an immune hub during infection, integrating local immune signals to orchestrate the immune response

Single-cell RNA-sequencing of PBMCs in Rheumatoid Arthritis and Rheumatoid Arthritis-Associated Interstitial Lung Disease

- Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a severe extra-articular manifestation of RA that affects up to 15% of RA patients.

- RA-ILD is a major driver of increased morbidity, mortality and increased healthcare utilization.

- There has been limited investigation of cellular biomarkers that may shed light on RA-ILD pathogenesis and progression.

- In this study, we use single-cell RNA sequencing to identify cellular biomarkers associated with the development of RA-ILD.

- We investigate the cellular signatures associated with the development of RA-ILD and its fibrotic and inflammatory subtypes in peripheral blood mononuclear cells (PBMC) samples from patients with RA-ILD using the Flex assay.

- The 10x Genomics Gene Expression Flex protocol allows the single cell profiling of fixed or frozen samples which preserves fragile cell types and streamlines the workflow of sample processing.

- Our findings will further elucidate key pathogenic mechanisms in the development of RA-ILD and identify peripheral blood biomarkers to improve future screening and treatment strategies.

Q & A

This Q & A session is your chance to ask any burning questions Q&A