RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus

Spatial transcriptomics aims to understand how the ensemble of RNA molecules in tissues and cells is organized in 3D space. Here we introduce Proximity RNA-seq, which identifies co-localization preferences for pairs or groups of chromatin-associated, nuclear-retained and nascent RNAs in cell nuclei. Proximity RNA-seq is based on massive-throughput RNA barcoding of sub-nuclear particles in water-in-oil emulsion droplets, followed by sequencing. Overall design: 4 Proximity RNA-Seq datasets (Pools 2, 5, 7 & 8), 2 Hi-C datasets