Please use this identifier to cite or link to this item: https://doi.org/10.1016/j.celrep.2019.01.041
Title: RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types
Authors: Monaco, G.
Lee, B.
Xu, W.
Mustafah, S.
Hwang, Y.Y.
Carré, C.
Burdin, N.
Visan, L.
Ceccarelli, M.
Poidinger, M.
Zippelius, A.
Pedro de Magalhães, J.
Larbi, A. 
Keywords: deconvolution
flow cytometry
gene modules
housekeeping
immune system
mRNA abundance
mRNA composition
mRNA heterogeneity
RNA-seq
transcriptome
Issue Date: 2019
Publisher: Elsevier B.V.
Citation: Monaco, G., Lee, B., Xu, W., Mustafah, S., Hwang, Y.Y., Carré, C., Burdin, N., Visan, L., Ceccarelli, M., Poidinger, M., Zippelius, A., Pedro de Magalhães, J., Larbi, A. (2019). RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types. Cell Reports 26 (6) : 1627-16400000000. ScholarBank@NUS Repository. https://doi.org/10.1016/j.celrep.2019.01.041
Rights: Attribution-NonCommercial-NoDerivatives 4.0 International
Abstract: The molecular characterization of immune subsets is important for designing effective strategies to understand and treat diseases. We characterized 29 immune cell types within the peripheral blood mononuclear cell (PBMC) fraction of healthy donors using RNA-seq (RNA sequencing) and flow cytometry. Our dataset was used, first, to identify sets of genes that are specific, are co-expressed, and have housekeeping roles across the 29 cell types. Then, we examined differences in mRNA heterogeneity and mRNA abundance revealing cell type specificity. Last, we performed absolute deconvolution on a suitable set of immune cell types using transcriptomics signatures normalized by mRNA abundance. Absolute deconvolution is ready to use for PBMC transcriptomic data using our Shiny app (https://github.com/giannimonaco/ABIS). We benchmarked different deconvolution and normalization methods and validated the resources in independent cohorts. Our work has research, clinical, and diagnostic value by making it possible to effectively associate observations in bulk transcriptomics data to specific immune subsets. © 2019 The AuthorsMonaco et al. generate an RNA-seq dataset on 29 immune cell types and identify modules of cell type-specific, co-expressed, and housekeeping genes. The mRNA heterogeneity and abundance of the different cell types were examined. Absolute deconvolution of PBMCs was obtained by taking into account mRNA abundance when normalizing the signature matrix. © 2019 The Authors
Source Title: Cell Reports
URI: https://scholarbank.nus.edu.sg/handle/10635/212327
ISSN: 22111247
DOI: 10.1016/j.celrep.2019.01.041
Rights: Attribution-NonCommercial-NoDerivatives 4.0 International
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