Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm
Summary: 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 filte...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725000310 |
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| author | Lin Du Jingmin Kang Jie Li Hua Qin Yong Hou Hai-Xi Sun |
| author_facet | Lin Du Jingmin Kang Jie Li Hua Qin Yong Hou Hai-Xi Sun |
| author_sort | Lin Du |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-4ddaef7deb9c4303b1de977bf2bcb9fb |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-4ddaef7deb9c4303b1de977bf2bcb9fb2025-02-06T05:12:49ZengElsevierSTAR Protocols2666-16672025-03-0161103625Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithmLin Du0Jingmin Kang1Jie Li2Hua Qin3Yong Hou4Hai-Xi Sun5College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Beijing 102601, ChinaBGI Research, Beijing 102601, China; BGI Research, Shenzhen 518083, ChinaBGI Research, Beijing 102601, ChinaBGI Research, Beijing 102601, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Beijing 102601, China; BGI Research, Shenzhen 518083, China; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725000310BioinformaticsHealth SciencesSystems biologyComputer sciences |
| spellingShingle | Lin Du Jingmin Kang Jie Li Hua Qin Yong Hou Hai-Xi Sun Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm STAR Protocols Bioinformatics Health Sciences Systems biology Computer sciences |
| title | Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm |
| title_full | Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm |
| title_fullStr | Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm |
| title_full_unstemmed | Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm |
| title_short | Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm |
| title_sort | protocol to denoise spatially resolved transcriptomics data utilizing optimal transport based gene filtering algorithm |
| topic | Bioinformatics Health Sciences Systems biology Computer sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725000310 |
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