Deconvolution Tactics and Normalization in Renal Spatial Transcriptomics
The kidney is composed of heterogeneous groups of epithelial, endothelial, immune, and stromal cells, all in close anatomic proximity. Spatial transcriptomic technologies allow the interrogation of in situ expression signatures in health and disease, overlaid upon a histologic image. However, some s...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Physiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fphys.2021.812947/full |
| _version_ | 1819364625217486848 |
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| author | Ricardo Melo Ferreira Benjamin J. Freije Michael T. Eadon |
| author_facet | Ricardo Melo Ferreira Benjamin J. Freije Michael T. Eadon |
| author_sort | Ricardo Melo Ferreira |
| collection | DOAJ |
| description | The kidney is composed of heterogeneous groups of epithelial, endothelial, immune, and stromal cells, all in close anatomic proximity. Spatial transcriptomic technologies allow the interrogation of in situ expression signatures in health and disease, overlaid upon a histologic image. However, some spatial gene expression platforms have not yet reached single-cell resolution. As such, deconvolution of spatial transcriptomic spots is important to understand the proportion of cell signature arising from these varied cell types in each spot. This article reviews the various deconvolution strategies discussed in the 2021 Indiana O’Brien Center for Microscopy workshop. The unique features of Seurat transfer score methodology, SPOTlight, Robust Cell Type Decomposition, and BayesSpace are reviewed. The application of normalization and batch effect correction across spatial transcriptomic samples is also discussed. |
| first_indexed | 2024-12-24T23:01:55Z |
| format | Article |
| id | doaj.art-b65d772ab452482d935f53748c0a8566 |
| institution | Directory Open Access Journal |
| issn | 1664-042X |
| language | English |
| last_indexed | 2024-12-24T23:01:55Z |
| publishDate | 2022-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Physiology |
| spelling | doaj.art-b65d772ab452482d935f53748c0a85662022-12-21T16:35:07ZengFrontiers Media S.A.Frontiers in Physiology1664-042X2022-01-011210.3389/fphys.2021.812947812947Deconvolution Tactics and Normalization in Renal Spatial TranscriptomicsRicardo Melo FerreiraBenjamin J. FreijeMichael T. EadonThe kidney is composed of heterogeneous groups of epithelial, endothelial, immune, and stromal cells, all in close anatomic proximity. Spatial transcriptomic technologies allow the interrogation of in situ expression signatures in health and disease, overlaid upon a histologic image. However, some spatial gene expression platforms have not yet reached single-cell resolution. As such, deconvolution of spatial transcriptomic spots is important to understand the proportion of cell signature arising from these varied cell types in each spot. This article reviews the various deconvolution strategies discussed in the 2021 Indiana O’Brien Center for Microscopy workshop. The unique features of Seurat transfer score methodology, SPOTlight, Robust Cell Type Decomposition, and BayesSpace are reviewed. The application of normalization and batch effect correction across spatial transcriptomic samples is also discussed.https://www.frontiersin.org/articles/10.3389/fphys.2021.812947/fullspatial transcriptomicsvisium gene expressionsingle nuclear RNA sequencingnephronacute kidney injurybiopsy specimen |
| spellingShingle | Ricardo Melo Ferreira Benjamin J. Freije Michael T. Eadon Deconvolution Tactics and Normalization in Renal Spatial Transcriptomics Frontiers in Physiology spatial transcriptomics visium gene expression single nuclear RNA sequencing nephron acute kidney injury biopsy specimen |
| title | Deconvolution Tactics and Normalization in Renal Spatial Transcriptomics |
| title_full | Deconvolution Tactics and Normalization in Renal Spatial Transcriptomics |
| title_fullStr | Deconvolution Tactics and Normalization in Renal Spatial Transcriptomics |
| title_full_unstemmed | Deconvolution Tactics and Normalization in Renal Spatial Transcriptomics |
| title_short | Deconvolution Tactics and Normalization in Renal Spatial Transcriptomics |
| title_sort | deconvolution tactics and normalization in renal spatial transcriptomics |
| topic | spatial transcriptomics visium gene expression single nuclear RNA sequencing nephron acute kidney injury biopsy specimen |
| url | https://www.frontiersin.org/articles/10.3389/fphys.2021.812947/full |
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