title: The correlation between expression profiles measured in single cells and in traditional bulk samples.
abstract: Reverse transcription quantitative PCR (RT-qPCR) is already an established tool for mRNA detection and quantification. Since recently, this technique has been successfully employed for gene expression analyses, and also in individual cells (single cell RT-qPCR). Although the advantages of single cell measurements have been proven several times, a study correlating the expression measured on single cells, and in bulk samples consisting of a large number of cells, has been missing. Here, we collected a large data set to explore the relation between gene expression measured in single cells and in bulk samples, reflected by qPCR Cq values. We measured the expression of 95 genes in 12 bulk samples, each containing thousands of astrocytes, and also in 693 individual astrocytes. Combining the data, we described the relation between Cq values measured in bulk samples with either the percentage of the single cells that express the given genes, or the average expression of the genes across the single cells. We show that data obtained with single cell RT-qPCR are fully consistent with measurements in bulk samples. Our results further provide a base for quality control in single cell expression profiling, and bring new insights into the biological process of cellular expression.
authors.affiliation: Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic.|2nd Faculty of Medicine, Charles University, Prague, Czech Republic.
authors.forename: David
authors.initials: D
authors.lastname: Dzamba
authors.affiliation: Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, BIOCEV, Vestec, Czech Republic.
authors.forename: Lukas
authors.initials: L
authors.lastname: Valihrach
authors.affiliation: Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, BIOCEV, Vestec, Czech Republic.
authors.forename: Mikael
authors.initials: M
authors.lastname: Kubista
authors.affiliation: Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic.|2nd Faculty of Medicine, Charles University, Prague, Czech Republic.
authors.forename: Miroslava
authors.initials: M
authors.lastname: Anderova
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D005904:Glial Fibrillary Acidic Protein / Q000235:genetics; D049452:Green Fluorescent Proteins / Q000235:genetics; D051379:Mice; D008822:Mice, Transgenic; D012333:RNA, Messenger / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D059010:Single-Cell Analysis
chemical_list: D005904:Glial Fibrillary Acidic Protein; D012333:RNA, Messenger; C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins