Faculty, Staff and Student Publications
Language
English
Publication Date
2-1-2025
Journal
Nature Communications
DOI
10.1038/s41467-025-56623-1
PMID
39893178
PMCID
PMC11787294
PubMedCentral® Posted Date
2-1-2025
PubMedCentral® Full Text Version
Post-print
Abstract
The variation of transcriptome size across cell types significantly impacts single-cell RNA sequencing (scRNA-seq) data normalization and bulk RNA-seq cellular deconvolution, yet this intrinsic feature is often overlooked. Here we introduce ReDeconv, a computational algorithm that incorporates transcriptome size into scRNA-seq normalization and bulk deconvolution. ReDeconv introduces a scRNA-seq normalization approach, Count based on Linearized Transcriptome Size (CLTS), which corrects differential expressed genes typically misidentified by standard count per 10 K normalization, as confirmed by orthogonal validations. By maintaining transcriptome size variation, CLTS-normalized scRNA-seq enhances the accuracy of bulk deconvolution. Additionally, ReDeconv mitigates gene length effects and models expression variances, thereby improving deconvolution outcomes, particularly for rare cell types. Evaluated with both synthetic and real datasets, ReDeconv surpasses existing methods in precision. ReDeconv alters the practice and provides a new standard for scRNA-seq analyses and bulk deconvolution. The software packages and a user-friendly web portal are available.
Keywords
Single-Cell Analysis, Algorithms, Transcriptome, RNA-Seq, Humans, Software, Gene Expression Profiling, Sequence Analysis, RNA, Animals, Computational Biology, Single-Cell Gene Expression Analysis, Statistical methods, Software
Published Open-Access
yes
Recommended Citation
Lu, Songjian; Yang, Jiyuan; Yan, Lei; et al., "Transcriptome Size Matters for Single-Cell RNA-Seq Normalization and Bulk Deconvolution" (2025). Faculty, Staff and Student Publications. 982.
https://digitalcommons.library.tmc.edu/uthshis_docs/982