Spatial Transcriptomics Sequencing of Mouse Liver at 2µm Resolution Using a Novel Spatial DNA Chip

Abstract

AbstractSpatial transcriptomics has showcased its efficacy in deciphering the intricate relationships between individual cells and tissues. We present spatial transcriptomics data using a novel high-resolution DNA chip with a capture region feature size of 2 x 2µm. Feature-to-feature gap space is zero, maximizing the capture area. Chips are manufactured at wafer scale using photolithography and are transferred to hydrogels, making them compatible with existing sample preparation and analysis workflows for fresh frozen or paraffin-embedded samples. For this report, we examined a fresh frozen sample from adult mouse liver. Using a bin size of 10, representing a 20µm x 20µm capture area, at 69% sequencing saturation, we obtained over 600 million unique mapped reads, the median number of unique reads captured was over 8,000 per region, demonstrating potential for additional unique reads with deeper sequencing. This high-resolution mapping of liver cell types and visualization of gene expression patterns demonstrates significant advances in spatial sequencing technology.