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SpotClean adjusts for spot swapping in spatial transcriptomics data

ABSTRACT: SpotClean adjusts for spot swapping in spatial transcriptomics data

PROVIDER: PRJNA737791 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14816682.fastq.gz	Fastqsanger.gz
	SRR14816683.fastq.gz	Fastqsanger.gz
	SRR14816684.fastq.gz	Fastqsanger.gz
	SRR14816685.fastq.gz	Fastqsanger.gz
	SRR14816686.fastq.gz	Fastqsanger.gz

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SpotClean adjusts for spot swapping in spatial transcriptomics data

Project description:Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. We conduct chimeric experiments to evaluate the spot swapping effect in 10x Visium spatial transcriptomics protocol. We propose SpotClean to adjust for spot swapping and, in doing so, to increase the sensitivity and precision with which downstream analyses are conducted.

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