Science Events in Vancouver
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Seminar: Single-Cell RNA Sequencing with Split-Pool Barcoding from the Brain to Bacteria
June 17, 2020 - 3:00 pm - 4:00 pm
Michael Smith Laboratories presents a seminar by
Dr. Georg Seelig
Associate Professor
Department of Electrical Engineering and Computer Science & Engineering
University of Washington
Hosted by Thibault Mayor
“Single-cell RNA sequencing with split-pool barcoding from the brain to bacteria”
Abstract:
To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq eliminates the need to isolate single cells, is compatible with fixed cells or nuclei, allows efficient sample multiplexing, and requires no customized equipment. We initially used SPLiT-seq to analyze over 150,000 single-nucleus transcriptomes from mouse brain and spinal cord. More than 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system.
More recently, we have adapted SPLiT-seq to work with bacteria, resulting in the first high-throughput scRNA-seq technology for microbes. We tested out method on both gram positive (B. subtilis) and gram negative (E. coli) bacteria and validate it using heat shock treatment. We then apply it to investigate the transition from exponential growth to stationary phase in B. subtilis. We not only find detailed gene expression profiles associated with known (and rare) states such as competence but also identify novel and unexpected gene expression states such as a sub-population associated with inositol metabolism that appears to be controlled through a bistable switch network.
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Meeting ID: 944 7599 4344
