Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue

Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue

Abstract We define and identify a new class of control genes for next-generation sequencing called total RNA expression genes (TREGs), which correlate with total RNA abundance in cell types of different sizes and transcriptional activity. We provide a data-driven method to identify TREGs from single...

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Bibliographic Details
Main Authors: Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Stephanie C. Page, Stephanie C. Hicks, Kristen R. Maynard, Leonardo Collado-Torres
Format: Article
Language:English
Published: BMC 2023-10-01
Series:Genome Biology
Subjects:
RNA abundance
RNAscope
snRNA-seq
TREG
Deconvolution
Bioconductor
Online Access:https://doi.org/10.1186/s13059-023-03066-w
Description
Summary:Abstract We define and identify a new class of control genes for next-generation sequencing called total RNA expression genes (TREGs), which correlate with total RNA abundance in cell types of different sizes and transcriptional activity. We provide a data-driven method to identify TREGs from single-cell RNA sequencing data, allowing the estimation of total amount of RNA when restricted to quantifying a limited number of genes. We demonstrate our method in postmortem human brain using multiplex single-molecule fluorescent in situ hybridization and compare candidate TREGs against classic housekeeping genes. We identify AKT3 as a top TREG across five brain regions.
ISSN:1474-760X

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