This is a historic project which has previously made use of HPC facilities at Newcastle University.
For further information about this project, please contact:
This project investigates the immunological mechanisms underlying otitis media with effusion (OME) in young children using multi-modal single-cell and spatial genomics. Adenoid tissue samples from paediatric donors (aged 2–6 years) undergoing routine adenoidectomy have been profiled using single-cell RNA sequencing with CITE-seq surface protein quantification, paired B cell and T cell receptor sequencing, spatial transcriptomics (10X Visium), and multiplex immunofluorescence imaging.
The project focuses on defining the cellular composition of paediatric adenoid tissue, characterising age-associated developmental programmes within the immune compartment, and identifying disease-associated alterations in immune cell abundance, transcriptional state, and cell-cell communication in children with OME compared to controls.
Python / Jupyter notebooks for use of single cell RNA sequencing tools including scanpy, scVI, cell2location.
Analysis is performed in Python using Jupyter notebooks. The core single-cell analysis relies on the scanpy ecosystem for quality control, normalisation, dimensionality reduction, clustering, and differential expression. Specialised tools include cell2location for spatial deconvolution of Visium data, milopy for differential abundance testing using the Milo framework, LIANA for ligand-receptor interaction analysis, and scirpy for immune receptor repertoire analysis.
High-memory needed large single-cell datasets (~170,000 cells across 19 donors)
No GPU access is required due to prior model pre-training on a different cluster.