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Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.

Charting an organs' biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. Tangram can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomica

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Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.

> 商业许可源文 · EUROPE_PMC · [CC-BY](https://creativecommons.org/licenses/by/)

书目信息

  • 引用：Biancalani T, Scalia G, Buffoni L, Avasthi R, Lu Z, Sanger A, Tokcan N, Vanderburg CR, Segerstolpe Å, Zhang M, Avraham-Davidi I, Vickovic S, Nitzan M, Ma S, Subramanian A, Lipinski M, Buenrostro J, Brown NB, Fanelli D, Zhuang X, Macosko EZ, Regev A. (2021). Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nature methods. PMID 34711971 · PMC8566243 · DOI 10.1038/s41592-021-01264-7
  • 证据类型：PRIMARY_RESEARCH
  • 主题：rna-seq、single-cell、spatial-omics
  • 被引次数（采集时）：796
  • 原始记录：[Europe PMC](https://europepmc.org/article/MED/34711971)
  • 来源许可：[CC-BY](https://creativecommons.org/licenses/by/)

    • 作者摘要（按来源许可复用）

    Charting an organs' biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. Tangram can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomically integrated spatial map at single-cell resolution of the visual and somatomotor areas.

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    Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. · GeniOmics