Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies /631/1647/2017 /631/1647/2017/2079 technical-report

Zhana Haimon, Alon Volaski, Johannes Orthgiess, Sigalit Boura-Halfon, Diana Varol, Anat Shemer, Simon Yona, Binyamin Zuckerman, Eyal David, Louise Chappell-Maor, Ingo Bechmann, Martin Gericke, Igor Ulitsky, Steffen Jung*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

134 Scopus citations

Abstract

Transcriptome profiling is widely used to infer functional states of specific cell types, as well as their responses to stimuli, to define contributions to physiology and pathophysiology. Focusing on microglia, the brain's macrophages, we report here a side-by-side comparison of classical cell-sorting-based transcriptome sequencing and the 'RiboTag' method, which avoids cell retrieval from tissue context and yields translatome sequencing information. Conventional whole-cell microglial transcriptomes were found to be significantly tainted by artifacts introduced by tissue dissociation, cargo contamination and transcripts sequestered from ribosomes. Conversely, our data highlight the added value of RiboTag profiling for assessing the lineage accuracy of Cre recombinase expression in transgenic mice. Collectively, this study indicates method-based biases, reveals observer effects and establishes RiboTag-based translatome profiling as a valuable complement to standard sorting-based profiling strategies.

Original languageAmerican English
Pages (from-to)636-644
Number of pages9
JournalNature Immunology
Volume19
Issue number6
DOIs
StatePublished - 1 Jun 2018
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2018 The Author(s).

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