Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm

Le résumé fourni par la source

Spatially resolved transcriptomics (SRT) data contain intricate noise due to the diffusion of transcripts caused by tissue fixation, permeabilization, and cell lysis during the experiment. Here, we present a protocol for denoising SRT data using SpotGF, an optimal transport-based gene filtering algorithm, without modifying the raw gene expression. We describe steps for data preparation, SpotGF score calculation, filtering threshold determination, denoised data generation, and visualization. Our protocol enhances SRT quality and improves the performance of downstream analyses. For complete details on the use and execution of this protocol, please refer to Du et al. 1 • Steps to denoise SRT data without false positive signals and additional noise • Guidance on setting parameters for SpotGF to denoise a variety of SRT datasets • User-friendly and computationally efficient implementation of SpotGF Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Spatially resolved transcriptomics (SRT) data contain intricate noise due to the diffusion of transcripts caused by tissue fixation, permeabilization, and cell lysis during the experiment. Here, we present a protocol for denoising SRT data using SpotGF, an optimal transport-based gene filtering algorithm, without modifying the raw gene expression. We describe steps for data preparation, SpotGF score calculation, filtering threshold determination, denoised data generation, and visualization. Our protocol enhances SRT quality and improves the performance of downstream analyses.

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.