Non-Invasive Transcriptomics (Internship/Bachelor Thesis)

30.07.2024, Abschlussarbeiten, Bachelor- und Masterarbeiten

The chair of Neurobiological Engineering offers a position in the non-invasive transcriptomics project.

Background

RNA sequencing enables the study of gene regulation and the response of living systems to external and internal stimuli. Next-generation sequencing methods make it possible to get a comprehensive look into the whole repertoire of RNAs that are present in the cell. While the field has made tremendous progress in the past few years, one main concern is the consumptive nature of most RNA sequencing protocols, meaning that RNA sequencing leads to the cell being dissolved.

Description

The Westmeyerlab has developed an export system that enables the shuttling of endogenous RNA transcripts out of cells for sequencing while keeping the cell integrity intact. This enables us to probe the same cells at different points in time, making it possible to track changes in the transcriptome as cells respond to changes in the environment. Since this method is well suited to monitor developmental processes, we would like to explore the method in new contexts.

Scope of the Project

Current focus topics are:

• Temporally-resolved transcriptomics: Since longitudinal data is crucial for establishing causal links, we are interested in increasing the temporal resolution of the method.
• Clonal tracking: We want to increase the number of clones that we can monitor at the same time.
• Ultra-low RNA input: Since we want to keep the perturbation due to the measurement at a minimum, we are interested in optimizing the ultra-low input RNA sequencing pipeline.

Your Contribution

We are looking for someone that is interested to work at the intersection of bioengineering and bioinformatics.

• Optimizing the RNA sequencing protocol (wetlab focus)
• Data analysis for RNA sequencing datasets (bioinformatics focus)
• Improving the time resolution of the readout (both wetlab and bioinfo)

Requirements

• You are currently studying MBT, Biochemistry, Bioinformatics or have experience in the field
• You have wetlab experience or worked with RNA sequencing data
• You are interested in working at the cutting edge of bioengineering research

Kontakt: martin@westmeyerlab.org