Using RNA barcoding and sequencing to study cellular differentiation on a single-cell and population level

Kuut, Gunnar (2021): Using RNA barcoding and sequencing to study cellular differentiation on a single-cell and population level. Dissertation, LMU München: Faculty of Chemistry and Pharmacy

Abstract

RNA sequencing, along with single-cell RNA sequencing, has been gaining popularity in the last decade and a half. Numerous commercial and non-commercial methods to perform transcriptome analysis exist. Despite it being so widespread, setting up an RNA sequencing platform, especially a single-cell RNA sequencing platform, is not without its own pitfalls. In this work, we showed the capabilities of our improved single-cell and bulk sequencing platform – SCRB-seq, in detecting transcriptional changes in BLaER1 cells after PRR stimulation as well as differentiation changes in CD4+ T cells after TCR activation. This study highlights the difficulties in identifying T helper sub-types in complex samples using scRNA-seq and bulk RNA-seq. Two of the main problems: overlapping cytokine production, and the continuous population seems to be an inherent property of T cells on the transcriptome level.

• Item Type: Theses (Dissertation, LMU Munich)
• Keywords: RNA-seq, scRNA-seq, SCRB-seq, T helper cells, CD4+, BLaER1, PRR stimulation, LPS, dsDNA
• Subjects: 500 Natural sciences and mathematics; 500 Natural sciences and mathematics > 540 Chemistry and allied sciences
• Faculties: Faculty of Chemistry and Pharmacy
• Language: English
• Date of oral examination: 28. June 2021
• 1. Referee: Hornung, Veit
• Signature of the printed copy: 0001/UMC 28071