Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics

Purpose: Here, we describe a method, Array-seq, to repurpose classical oligonucleotide microarrays for spatial transcriptomics profiling. We demonstrate that Array-seq yields spatial transcriptomes with high detection sensitivity and localization specificity using histological sections from mouse tissues as test systems. Moreover, we show that the large surface area of Array-seq slides enables the generation of spatial transcriptomes at high throughput by profiling multi-organ sections, in three dimensions by processing serial sections from one sample, and across whole human organs using spleen sections. Experimental Methods: To generate Array-seq slides, we first obtain microarrays carrying custom-design probes that contain common sequences flanking unique barcodes at known coordinates. Second, we perform a simple, two-step reaction that produces mRNA capture probes across all spots on the microarray and thereby creates Array-seq slides set for spatial transcriptomics. Following in-situ mRNA capture, reverse transcription, libaray preparation, Array-seq libraries are sequenced using the Illumina sequencing-by-synthesis (SBS) platform. A total of 5 Array-seq experiments were run on the following tissues: (1) Mouse Main Olfactory Bulb (MOB), (2) Mouse kidney (4 replicates, adjacent sections used for Array-seq and Visium), (3) 3D Mouse kidney (100-μm spacing between 8 individual sections from a single kidney to generate a 3-dimensional dataset), (4) Multi-organ (A single Array-seq caputre area was used for 2 mouse brain sections, 3 mouse kidney sections, 3 mouse liver sections), (5) Whole mount human spleen section. 6-8 week old C57BL/6J mice were used for all mouse experiments.