Dresden 2017 – scientific programme

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BP: Fachverband Biologische Physik

BP 59: Multi-Cellular-Systems

BP 59.1: Invited Talk

Friday, March 24, 2017, 09:30–10:00, HÜL 386

Spatially-resolved transcriptomics and single-cell lineage tracing — •Jan Philipp Junker — Berlin Institute for Medical Systems Biology, MDC Berlin, Germany

Tissues and organs are complex mixtures of many different cell types, each of which is defined by a characteristic set of expressed genes. Systematic analysis of tissue architecture hence requires approaches that analyze gene expression on the single cell level. Recent progress in single-cell RNA sequencing now enables gene expression analysis of single cells on the level of the whole transcriptome, an important advance over microscopy-based methods that are typically limited to studying just one or a few genes at a time. However, information about the spatial position and lineage history of cells, which can be obtained by microscopy, is lost in sequencing experiments. Here, we present tomo-seq, a method that combines traditional histological techniques with low-input RNA sequencing and mathematical image reconstruction to generate a high-resolution genome-wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. Importantly, our technique allows searching for genes that are expressed in specific spatial patterns without manual image annotation. Furthermore, we introduce scartrace, a strategy for massively parallel clonal analysis in the zebrafish based on CRISPR/Cas9 technology. We exploit the fact that Cas9-induced generation of double-strand breaks leads to formation of short insertions or deletions (genetic scars), which are variable in their length and position. We demonstrate that these genetic scars are ideal cellular barcodes for lineage analysis.