The SpaRTAN Group (Spatially Resolved Transcriptomics At Newcastle) organised a general meeting between our 4 constituent units (The Human Developmental Biology Resource (HDBR), The Bio-Imaging Unit, The Genomics Core Facility, and The Bioinformatics Support Unit).

Spatial transcriptomics is a highly complex technique with the full workflow taking a number of weeks and hundreds of steps. SpaRTAN brings together experts from across Newcastle University in each of the necessary stages in order to offer a complete end-to-end service, from collecting samples to detailed analysis. 

This meeting was designed for new staff to introduce themselves and for each unit to give an overview on how their section of the pipeline currently works. This included talks from HDBR on sample preparation, initial QC, and the slide-based stages on the spatial transcriptomics workflow. This was followed by The Bio-Imaging Unit talking about image acquisition and issues that must be corrected at this stage. The Genomics Core Facility spoke about QC of the cDNA or ligated probe products they receive to ensure good library preparation. Finally, The Bioinformatics Support Unit ended the session by covering their QC measures of the read sequences and the various packages they use to complete the cell clustering and differential gene expression analysis that can be passed onto users.

Outcomes of the meeting included the potential use of a shared data repository for all SpaRTAN related data, a commitment to meet again in the near future for sessions going over each aspect in detail, lively discussion on parameters and technical limitations, as well as everyone getting to know each other a little better.