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Advancing Brain Barriers RNA Sequencing: Guidelines from Experimental Design to Publication

Francisco, David M. F. and Marchetti, Luca and Rodríguez-Lorenzo, Sabela and Frías-Anaya, Eduardo and Figueiredo, Ricardo M. and Winter, Peter and Romero, Ignacio Andres and de Vries, Helga E. and Engelhardt, Britta and Bruggmann, Rémy (2020) Advancing Brain Barriers RNA Sequencing: Guidelines from Experimental Design to Publication. Fluids and Barriers of the CNS, 17. pp. 1-33. ISSN 2045-8118

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Abstract

Background: RNA sequencing (RNA-Seq) in its varied forms has become an indispensable tool for analyzing diferential gene expression and thus characterization of specifc tissues. Aiming to understand the brain barriers genetic signature, RNA seq has also been introduced in brain barriers research. This has led to availability of both, bulk and single-cell RNA-Seq datasets over the last few years. If appropriately performed, the RNA-Seq studies provide powerful datasets that allow for signifcant deepening of knowledge on the molecular mechanisms that establish the brain barriers. However, RNA-Seq studies comprise complex workfows that require to consider many options and variables before, during and after the proper sequencing process. Main body: In the current manuscript, we build on the interdisciplinary experience of the European PhD Training Network BtRAIN (https://www.btrain-2020.eu/) where bioinformaticians and brain barriers researchers collaborated to analyze and establish RNA-Seq datasets on vertebrate brain barriers. The obstacles BtRAIN has identifed in this process have been integrated into the present manuscript. It provides guidelines along the entire workfow of brain barriers RNA-Seq studies starting from the overall experimental design to interpretation of results. Focusing on the vertebrate endothelial blood–brain barrier (BBB) and epithelial blood-cerebrospinal-fuid barrier (BCSFB) of the choroid plexus, we provide a step-by-step description of the workfow, highlighting the decisions to be made at each step of the workfow and explaining the strengths and weaknesses of individual choices made. Finally, we propose recommendations for accurate data interpretation and on the information to be included into a publication to ensure appropriate accessibility of the data and reproducibility of the observations by the scientifc community. Conclusion: Next generation transcriptomic profling of the brain barriers provides a novel resource for understanding the development, function and pathology of these barrier cells, which is essential for understanding CNS homeostasis and disease. Continuous advancement and sophistication of RNA-Seq will require interdisciplinary approaches between brain barrier researchers and bioinformaticians as successfully performed in BtRAIN. The present guidelines are built on the BtRAIN interdisciplinary experience and aim to facilitate collaboration of brain barriers researchers with bioinformaticians to advance RNA-Seq study design in the brain barriers community.

Item Type: Article
Additional Information: A cikk szerzői között szerepelnek a BtRAIN Network kutatói is. Magyar tagok: Ana Raquel Santa Maria és Deli Mária A.
Subjects: R Medicine / orvostudomány > RC Internal medicine / belgyógyászat > RC0321 Neuroscience. Biological psychiatry. Neuropsychiatry / idegkórtan, neurológia, pszichiátria
SWORD Depositor: MTMT SWORD
Depositing User: MTMT SWORD
Date Deposited: 01 Dec 2020 11:30
Last Modified: 01 Dec 2020 11:30
URI: http://real.mtak.hu/id/eprint/117635

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