Single Cell and Spatial Technologies

Single Cell Technologies Platform

Single-cell technologies permit the analysis of each cell as a unique entity, providing a detailed understanding of cellular heterogeneity within a tissue and revealing the molecular and functional characteristics that define cell identity.

At IKMB, we are dedicated to deciphering the diversity of cellular processes at the single-cell level. Our platform for single-cell technologies produces high-quality genetic, transcriptomic, proteomic, and epigenetic profiles of individual cells, with the aid of cutting-edge computational methods for in-depth analysis.

What is Single Cell Technology?

Single-cell technologies have revolutionized our understanding of cellular biology by providing unprecedented insights into the heterogeneity, dynamics, and function of cells within tissues. These technologies have advanced our ability to study complex biological systems, such as tissues and organs, at a resolution that was not previously possible with bulk analyses. Examples of single-cell omics technologies include single-cell RNA sequencing (scRNA-seq), single-cell proteomics, and single-cell epigenomics.

What are the applications?

The power of single-cell technologies extends across a wide range of biomedical disciplines. In immunology, we can investigate the diversity of immune cell populations and their roles in fighting infections and autoimmune diseases. Moreover, single-cell technologies allow us to capture the development of cell states over time and identify the factors that drive these transitions. Thus, potentially identifying the mechanisms of cellular differentiation, development, and disease progression.

Our Single Cell Technology Platform

Our platform has experience working with samples from different tissues of human and other model systems. With a dedicated multi-disciplinary team, we have been involved in the development and standardization this technology in different tissue samples. And have had successful publications of our datasets; from linking key cell types to severe COVID-19 disease trajectory (Bernardes et al. 2020), as well as low-avidity T cells (Bacher et al. 2020).

Sample Preparation and Cell Dissociation

Whether working with fresh or frozen tissues, our team possesses extensive expertise in handling samples that are notoriously challenging to process, specifically those from the brain and intestinal epithelium. We have successfully led numerous projects involving these complex samples, demonstrating a deep understanding and the necessary instrumental capabilities to overcome the technological challenges associated with single-cell experiments.

Library Generation and Sequencing

With dedicated people with years of experience in library preparation, and availability of both 10x Chromium Controller and Chromium X series instruments in our facility, we are offering the following single cell solutions:

3′ expression tags
5′ expression tags
V(D)J sequencing
T and/or B-cell specific expression tags
ATAC/and Multiome

This platform is powered by the DFG-funded NGS core facility “Comprehensive Center for Genomic Analysis” (CCGA), allowing standardized sequencing workflows at best quality. The main sequencing instrument for the current spatial transcriptomics methods is the Illumina NovaSeq 6000.

Data Analysis and Visualization

Our bioinformatics team offers comprehensive and expert analytics support for single-cell research. From data preprocessing to integration of multiple datasets/samples to cell annotation. As well as more advanced analytic methods like differential expression and coexpression analysis and gene set enrichment analysis. Leading to comprehensive interpretations of single-cell datasets and empowering groundbreaking discoveries.

Technician:
Sabine Kock

Contact:
Joana Pimenta Bernardes

For detailed information:
CCGA-Homepage

Spatial Transcriptomics Platform

Spatial omics technologies allow researchers to analyze the molecular composition of cells and their interactions in a spatial context, providing insights into the organization of tissues and helping understand the complexity of biological systems.

At IKMB, we are committed to unraveling the spatial organization of cellular processes within tissues of interest, e.g. intestinal epithelium. Our spatial platform enables us to generate high-quality transcriptomics data from tissue samples, which we analyze using state-of-the-art computational methods.

What is Spatial Technology?

Spatial technology is a revolutionary approach that combines transcriptomics with spatial information. By measuring gene expression levels at individual cells or subcellular compartments within intact tissue sections, we can uncover its cellular heterogeneity and tissue dynamics. This information can reveal previously hidden insights into the relationships between cells, tissues, and organs, providing a deeper understanding of biological processes and disease mechanisms.

What are the applications?

Spatial technology can further our understanding of the spatial distribution of immune-related genes. Thus, shedding light on the interplay of different contributors of inflammatory disease such as immune cells, and immune cell interactions. Furthermore, these applications are able to identify potential drug targets by revealing the spatial distribution of genes associated with specific cellular functions, which can guide the development of targeted therapies.

Our Spatial Technology Platform

Our platform was built onto our decades-long expertise in histological analysis, with the team and instruments essential for a successful workflow. Currently, we offer following workflows and technologies:

Sample Preparation and Tissue Sectioning

Our long-standing experience with histological methods enables efficient and standardized tissue preparation for spatial omics generation from a wide range of sample types, including fixed and unfixed tissues, biopsies, and complex mixtures.

Library Generation and Sequencing

With the availability of a 10x Visium CyAssist instrument in our facility, we are offering following spatial transcriptomics solutions:

10x Visium Spatial Transcriptomics for OCT-embedded tissue (any species)
10x Visium Spatial Transcriptomics for FFPE tissue (mouse, human) *
10x Visium Spatial Proteogenomics for FFPE tissue (human) *

* Workflows require the 10x Visium CytAssist

Data Analysis and Visualization

Our team provides expertises in analyzing spatial gene expression patterns and generating high-resolution maps of tissue organization. The analysis portfolio includes deconvolution methods based on scRNA-seq datasets and neighborhood analysis to identify spatial cell-cell interactions. Coupled with precise histopathological annotations, these methods link novel molecular insights with morphologic features in the disease-relevant tissues.

Contact: Florian Tran