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

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

PROVIDER: PRJNA1106443 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28850500_1.fastq.gz	Fastqsanger.gz
	SRR28850500_2.fastq.gz	Fastqsanger.gz
	SRR28850600_1.fastq.gz	Fastqsanger.gz
	SRR28850600_2.fastq.gz	Fastqsanger.gz
	SRR28850501_1.fastq.gz	Fastqsanger.gz

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Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics

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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.

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