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Analysis of single cell RNA seq data to identify markers for subtyping of non-small cell lung cancer
University of Skövde, School of Bioscience.
2020 (English)Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Single cell RNA technology is a recent technical advancement used to understand the cancertumorgenicity at single cell resolution. In this study we have analyzed the scRNA data from thenon-small cell lung cancer (NSCLC) dataset to facilitate the early identification of NSCLCsubtypes namely, squamous cell carcinoma (SCC) and adenocarcinoma (AC). Non-immunecells, have a major role in tumorigenesis of the malignant tumors, in early stages. Therefore,we have analyzed the major non-immune cells, namely endothelial cells and fibroblast cellsfrom the GSE127465 dataset using SEURAT pipeline. Dimensionality reduction analysis andcluster analysis indicate that AC and SCC subtypes of NSCLC have different fibroblastcompositions. Differential gene expression analysis indicates that AC tumours have shownelevated content of MGP/PTGDS and INMT/MFAP4 fibroblast cells, whereas squamous cellcarcinoma showed an elevated content of COL6A1/COL6A2 and FNDC1/COL12A1 fibroblastcells. The statistical analysis shows that the clustering is statistically significant and not anartefact. Given that the tumour microenvironment is highly dynamic, in this study we haveattempted to understand the tumour microenvironment by scRNA analysis of non-immune cellsat single cell resolution.

Place, publisher, year, edition, pages
2020. , p. 39
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:his:diva-18514OAI: oai:DiVA.org:his-18514DiVA, id: diva2:1440501
Subject / course
Bioinformatics
Educational program
Bioinformatics - Master’s Programme
Supervisors
Examiners
Available from: 2020-06-15 Created: 2020-06-15 Last updated: 2020-06-15Bibliographically approved

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CiteExportLink to record
Permanent link

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Citation style
  • apa
  • apa-cv
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
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  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
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  • asciidoc
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