Analysing single cell RNA sequencing data of the developing brain: a bioinformatic project hos Københavns Universitet

Aim: To identify differentially expressed genes across cortical layers in the developing brain in an effort to understand mechanisms regulating development.

Project length: 6-12 months

Our lab has identified that one region of the brain, the entorhinal cortex (responsible for processing spatial memory) develops differently than other cortical regions. Traditionally, the brain develops in an inside-out pattern. Instead, we find the entorhinal cortex develops either by a sandwich pattern or by parallel lamination. We wish to identify genes that regulate this altered development pattern. We have performed single cell RNA sequencing on the developing brain and this project will seek to process the data using different scRNAseq computational tools (e.g. Seurat, RNA velocity) to identify gene candidates to pursue in follow up experiments.

Your knowledge and expertise:

Have a good working knowledge and experience in using software including: R, python and are confident in creating your own scripts.

Techniques/Software learned:

Normalization of single cell RNA seq data

scRNAseq pipeline and tools, CellRanger and Loupe Browser


RNA velocity tool, Velocyto


Supervisor: Associate Professor Vanessa Hall Contact:

Our group and research: The Group for Brain Development and Disease is an inclusive and diverse research group that is composed of local and international researchers of varying age and background. The group collaborates with leading experts in a variety of different fields (bioinformaticians, neuroanatomists and developmental biologists and imaging experts) both nationally and internationally. It is expected that all group members thrive on achieving excellence, are an active team member and respect their peers and colleagues, irrespective of their gender or background. The group leader is also director of a non-profit organization that addresses gender inequality issues in academia and this is high on the priority list for her own research group. The group’s values include, providing positive feedback, rewarding excellence, envision BIG if starting small, being passionate about research, that growth and learning is in our DNA and that it’s all about the people. The research group was established in 2017 and has over the last years focused on categorizing the developing entorhinal cortex using single cell RNA sequencing, bioinformatics, MRI, Diffusion Tensor Imaging and immunohistochemistry technologies. The group has discovered the genotypes of several cells within the entorhinal cortex and that the entorhinal cortex forms in a parallel pattern atypical of the inside out typical formation of the rest of the neocortex. The entorhinal cortex is the brain region in focus for the group, as it is “ground zero” for the emergence of Alzheimer’s disease pathology. Understanding the uniqueness and intricacies of this part of the brain is important for better understanding Alzheimer’s disease, which could lead to novel treatments in the future. For more info see the group’s research page:

Bemærk: Du skal ofte bruge forhåndsgodkendelse fra dit universitet eller studievejleder for at sikre, at projekter eller specialeopgaver på SDU Jobbank vil blive accepteret som en del af dit studie. Kontakt de relevante aktører i god tid for at sikre, at du vælger det rette projekt.