Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/140677
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Type: | Journal article |
Title: | Library size confounds biology in spatial transcriptomics data |
Author: | Bhuva, D.D. Tan, C.W. Salim, A. Marceaux, C. Pickering, M.A. Chen, J. Kharbanda, M. Jin, X. Liu, N. Feher, K. Putri, G. Tilley, W.D. Hickey, T.E. Asselin-Labat, M.-L. Phipson, B. Davis, M.J. |
Citation: | Genome Biology, 2024; 25(1):99-1-99-10 |
Publisher: | BMC |
Issue Date: | 2024 |
ISSN: | 1474-7596 1474-7596 |
Statement of Responsibility: | Dharmesh D. Bhuva, Chin Wee Tan, Agus Salim, Claire Marceaux, Marie A. Pickering, Jinjin Chen, Malvika Kharbanda, Xinyi Jin, Ning Liu, Kristen Feher, Givanna Putri, Wayne D. Tilley, Theresa E. Hickey, Marie-Liesse Asselin-Labat, Belinda Phipson, and Melissa J. Davis |
Abstract: | Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including normalization methods. Here, we demonstrate that library size is associated with tissue structure and that normalizing these effects out using commonly applied scRNA-seq normalization methods will negatively affect spatial domain identification. Spatial data should not be specifically corrected for library size prior to analysis, and algorithms designed for scRNA-seq data should be adopted with caution. |
Keywords: | Spatial molecular data disease microenvironments |
Rights: | © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the mate‑ rial. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdo‑ main/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
DOI: | 10.1186/s13059-024-03241-7 |
Grant ID: | http://purl.org/au-research/grants/nhmrc/2021286 http://purl.org/au-research/grants/nhmrc/GNT1175653 http://purl.org/au-research/grants/nhmrc/2021041 |
Published version: | http://dx.doi.org/10.1186/s13059-024-03241-7 |
Appears in Collections: | Research Outputs |
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File | Description | Size | Format | |
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hdl_140677.pdf | Published version | 4.48 MB | Adobe PDF | View/Open |
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