Single cell/nuclei analyses of adipose tissue
Whole tissue technologies	Pros	Cons
Single cell/nuclei sequencing (e.g., 10x Genomics and other droplet-based methods)	Unbiased profiling of all cells in tissue Genome-wide quantification of transcriptome/epigenome High throughput for detection of cellular heterogeneity and rare cell types Detection of cell fate trajectories	Stressful and biased isolation of cells/nuclei Ambient RNA contamination (esp. snRNA-seq) Limited sequencing depth Lack of spatial information
Sequencing-based spatial transcriptomics (e.g., GeoMx® Digital Spatial Profiler, Illumina Visium)	Spatial resolution of transcriptome Detection of tissue microregions Captures all cell types in tissue section Limited cross-contamination between cell types	Lack of full cellular resolution Adipocyte size and lipid content complicates transcriptome-to-cell assignment Limited sequencing depth Limited cell sampling per tissue sections
Hybridization/antibody-based spatial analyses (e.g., MERFISH, CosMx™, 10x Genomics Xenium)	Subcellular resolution of transcriptome/proteome in tissue Detection of tissue microregions Capture of all cell types in tissue section Limited cross-contamination between cell types	Lack of unbiased detection Limited detection depth Limited cell sampling per tissue sections