Detection of allele-specific expression in spatial transcriptomics with spASE
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framew...
| Main Authors: | , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Springer Science and Business Media LLC
2024
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| Online Access: | https://hdl.handle.net/1721.1/155698 |
| _version_ | 1824458142112546816 |
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| author | Zou, Luli S. Cable, Dylan M. Barrera-Lopez, Irving A. Zhao, Tongtong Murray, Evan Aryee, Martin J. Chen, Fei Irizarry, Rafael A. |
| author2 | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science |
| author_facet | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Zou, Luli S. Cable, Dylan M. Barrera-Lopez, Irving A. Zhao, Tongtong Murray, Evan Aryee, Martin J. Chen, Fei Irizarry, Rafael A. |
| author_sort | Zou, Luli S. |
| collection | MIT |
| description | Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein. |
| first_indexed | 2024-09-23T12:08:47Z |
| format | Article |
| id | mit-1721.1/155698 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2025-02-19T04:21:11Z |
| publishDate | 2024 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1556982025-01-04T05:24:19Z Detection of allele-specific expression in spatial transcriptomics with spASE Zou, Luli S. Cable, Dylan M. Barrera-Lopez, Irving A. Zhao, Tongtong Murray, Evan Aryee, Martin J. Chen, Fei Irizarry, Rafael A. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein. 2024-07-17T16:24:36Z 2024-07-17T16:24:36Z 2024-07-08 2024-07-14T03:17:25Z Article http://purl.org/eprint/type/JournalArticle 1474-760X https://hdl.handle.net/1721.1/155698 Zou, L.S., Cable, D.M., Barrera-Lopez, I.A. et al. Detection of allele-specific expression in spatial transcriptomics with spASE. Genome Biol 25, 180 (2024). PUBLISHER_CC en 10.1186/s13059-024-03317-4 Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ The Author(s) application/pdf Springer Science and Business Media LLC BioMed Central |
| spellingShingle | Zou, Luli S. Cable, Dylan M. Barrera-Lopez, Irving A. Zhao, Tongtong Murray, Evan Aryee, Martin J. Chen, Fei Irizarry, Rafael A. Detection of allele-specific expression in spatial transcriptomics with spASE |
| title | Detection of allele-specific expression in spatial transcriptomics with spASE |
| title_full | Detection of allele-specific expression in spatial transcriptomics with spASE |
| title_fullStr | Detection of allele-specific expression in spatial transcriptomics with spASE |
| title_full_unstemmed | Detection of allele-specific expression in spatial transcriptomics with spASE |
| title_short | Detection of allele-specific expression in spatial transcriptomics with spASE |
| title_sort | detection of allele specific expression in spatial transcriptomics with spase |
| url | https://hdl.handle.net/1721.1/155698 |
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