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ANC Workshop: Sam Heron, Chair: Jinli Hu

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Investigating Inter-Cellular Interaction: An in silico Method for Separation of Multi-Species RNA-Seq Datasets

What
  • ANC Workshop Talk
When Feb 23, 2016
from 11:00 AM to 12:00 PM
Where IF Room 4.31/4.33
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Separation of stem-cell cultures by cell-type to study inter-cellular interaction has previously been carried out via methods of physical separation in order to separately extract data from each cell-type. These processes frequently contaminate samples with non-target cells and introduce noise through triggering the over-expression of stress and apoptosis (cell-death) related genes.

A new experimental technique has recently been developed which involves the in vitro co-culturing of two cell types using stem cells of closely related species with the aim of separating the resultant RNA-Seq data in silico relying on genomic difference.

I will briefly introduce this technique before detailing the in silico method that I have developed to separate this data by species and thus by cell type, enabling the downstream study of transcriptomic interaction between these cell-types. I will discuss the present state of this method detailing preliminary results and projected improvements that will allow for a more in depth analysis of this type of RNA-Seq data.