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Dr. Stefania Giacomello, Division of Gene Technology, Biotechnology, KTH

Spatial Transcriptomics and its applications: from mammals to plants

Time: Thu 2016-03-17 09.00 - 11.00

Location: FA31

Participating: Dr. Stefania Giacomello

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Title: Spatial Transcriptomics and its applications: from mammals to plants

Abstract: Knowledge of the spatial patterning of gene expression is key to advancing our understanding of numerous biological processes. However, current methods do not provide a spatial context as they profile expression at the cell population level. Such spatial information is a key aspect in several biological and medical experiments. Spatial Transcriptomics is a novel method developed in our research group which captures spatially resolved gene expression profiles within tissue micro-sections. The method has been successfully applied to mouse olfactory bulbs, breast cancer and plant tissues.

The method consists of placing tissue micro-sections onto arrays coated with barcoded probes specific for capturing mRNA. Barcodes are used to spatially locate an mRNA within the tissue micro-section and are clustered with a resolution of 100 μm. Captured mRNA is then reverse transcribed, cDNA is removed from the array and used to prepare ad hoc Illumina sequencing libraries.

A detailed overview of the method workflow will be presented, as well as its application on tissue of interests with particular focus on plant tissues.

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Belongs to: Department of Applied Physics
Last changed: Mar 16, 2016