MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics.

Autor:	Martin N; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Olsen P; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Quon J; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Campos J; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Cuevas NV; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Nagra J; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., VanNess M; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Maltzer Z; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Gelfand EC; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Oyama A; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Gary A; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Wang Y; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Alaya A; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Ruiz A; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Reynoldson C; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Bielstein C; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Pom CA; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Huang C; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Slaughterbeck C; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Liang E; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Alexander J; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Ariza J; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Malone J; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Melchor J; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Colbert K; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Brouner K; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Shulga L; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Reding M; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Latimer P; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Sanchez R; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Barta S; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Egdorf T; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Madigan Z; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Pagan CM; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Close JL; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Long B; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Kunst M; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Lein ES; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Zeng H; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., McMillen D; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA., Waters J; Allen Institute for Brain Science, 615 Westlake Ave N, Seattle WA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Dec 07. Date of Electronic Publication: 2024 Dec 07.
DOI:	10.1101/2024.12.04.626766
Abstrakt:	Image-based spatial transcriptomics platforms are powerful tools often used to identify cell populations and describe gene expression in intact tissue. Spatial experiments return large, high-dimension datasets and several open-source software packages are available to facilitate analysis and visualization. Spatial results are typically imperfect. For example, local variations in transcript detection probability are common. Software tools to characterize imperfections and their impact on downstream analyses are lacking so the data quality is assessed manually, a laborious and often a subjective process. Here we describe imperfections in a dataset of 641 fresh-frozen adult mouse brain sections collected using the Vizgen MERSCOPE. Common imperfections included the local loss of tissue from the section, tissue outside the imaging volume due to detachment from the coverslip, transcripts missing due to dropped images, varying detection probability through space, and differences in transcript detection probability between experiments. We describe the incidence of each imperfection and the likely impact on the accuracy of cell type labels. We develop MerQuaCo, open-source code that detects and quantifies imperfections without user input, facilitating the selection of sections for further analysis with existing packages. Together, our results and MerQuaCo facilitate rigorous, objective assessment of the quality of spatial transcriptomics results.
Databáze:	MEDLINE
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