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Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics - Bulk RNA-seq

ABSTRACT: Bulk RNA-seq (PME-seq) generated for analysis in parallel with Array-seq.

ORGANISM(S): Mus musculus

PROVIDER: GSE266246 | GEO | 2024/11/14

REPOSITORIES: GEO

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Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics

Project description: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.

2024-11-14 | GSE266244 | GEO