Bioinformatics Seminars

Bioinformatics Seminar

Time: 11AM
Venue: Davis Auditorium and Teams

26 July 2022

Cell type annotations of single cell spatial transcriptomics CosMx data

Jinjin Chen
WEHI Bioinformatics

Recent advances in technology now allows transcriptomics information of single cells to be measured along with their spatial location in the tissue. Nanostring CosMx single molecular imager (SMI) is one of the latest technology which can provide such dataset for a targeted gene panel in FFPE and fresh frozen tissue samples. With most current cell type annotation methods developed based on single-cell RNAseq data, it will be of great interest to establish if these methods are transferable to the new spatial transcriptomics datasets (in this case CosMx SMI). To address this question, we have developed a workflow to test and compare these methods against different CosMX datasets. This workflow investigates 6 different cell annotation methods against two CosMx lung datasets. In this seminar, I will present the preliminary work I’ve done using this workflow to establish an ensembled approach to define cell types in CosMX SMI data. This is my 2nd year milestone seminar, and this work is a part of a larger collaborative project in the davis lab with collaborators in UQ (Queensland) and NanoString.

Search past seminars