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Methodology for single cell profiling using spatially resolved gene expression data.
KTH, School of Biotechnology (BIO).
2013 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
: Metod för singel cell analys av gen expression (Swedish)
Abstract [en]

The advent of single-cell transcriptomics has enabled the study of cellular eterogeneity within and among populations. Cuurent methods are only able to process a small number of cells. A promising method for high-througput spatially resolved gene expression analysis with close to songle-cell resolution os currently being developed under the concept of spatial transcriptomics. Work is currently carried out to create bioinformatics tools to enable efficient analysis and integration of the data produced by the method.

This thesis describes an automatized pipeline that has been developed for the integration and post-processing of spatial transcriptomics cell line imaging and sequencing data. The pipeline was applied to data from two different cell lines derived from a four-stage cancer model study. Suitable pipeline parameters for the analysis of these cell lines are proposed.

Place, publisher, year, edition, pages
2013.
Keyword [en]
Single cell RNA
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:kth:diva-150559OAI: oai:DiVA.org:kth-150559DiVA: diva2:744723
Supervisors
Examiners
Available from: 2015-04-17 Created: 2014-09-05 Last updated: 2015-09-22Bibliographically approved

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