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

Spatial transcriptomics enables deep exploration of cellular gene expression, making it possible to elucidate the relationship between individual cells and tissues, thus enabling researchers to better understand development and disease. In this study, we present spatial transcriptomics data using a novel high-resolution DNA chip with a capture region size of 6.5 x 6.5 mm containing 2 x 2 µm features for spatial barcoding with no gaps between them, thereby maximizing the capture area. These chips are manufactured at wafer scale using photolithography and are transferred to hydrogels, making them compatible with existing workflows for fresh frozen or paraffin-embedded samples. Herein, we examined a fresh frozen sample from an adult mouse liver. Using a bin size of 10, representing a 20 µm x 20 µm capture area, and at 68.78%, sequencing saturation, we obtained over 1.3 billion unique mapped reads, with a median of 16,967 unique reads per region, indicating the potential for more unique reads with deeper sequencing. This high-resolution mapping of liver cell types and the visualization of gene expression patterns illustrate significant advancements in spatial sequencing technology. A spatial transcriptomics assay was performed on a fresh frozen adult mouse liver sample to investigate spatially resolved gene expression. A high-resolution DNA chip with 2 µm × 2 µm features was used for spatial barcoding. The tissue section was processed through a spatial transcriptomics workflow, including RNA hybridization, reverse transcription, and cDNA synthesis. Sequencing was conducted on an Illumina NovaSeq 6000 platform, providing detailed insights into liver cell type zonation and spatial gene expression patterns.