Comparative analysis of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing
Spatial transcriptomics extends single cell RNA sequencing (scRNA-seq) by providing spatial context for cell type identification and analysis. Imaging-based spatial technologies such as Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) can achieve single-cell resolution, directly mapping single cell identities to spatial positions. MERFISH produces an intrinsically different data type than scRNA-seq and a technical comparison between the two modalities is necessary to ascertain how to best integrate them. We performed MERFISH on mouse liver and kidney and compared the resulting bulk and single-cell RNA statistics with those from the Tabula Muris Senis cell atlas as well as from two Visium datasets. MERFISH quantitatively reproduced the bulk RNA-seq and scRNA-seq results with improvements in overall dropout rates and sensitivity. Finally, we found that MERFISH independently resolved distinct cell types and spatial structure in both liver and kidney. Computational integration with the Tabula Muris Senis atlas did not enhance these results. We conclude that compared to scRNA-seq, MERFISH provides a quantitatively comparable method for measuring single-cell gene expression and can robustly identify cell types without the need for computational integration with scRNA-seq reference atlases.