PT  - JOURNAL ARTICLE
AU  - Elisabetta Mereu
AU  - Atefeh Lafzi
AU  - Catia Moutinho
AU  - Christoph Ziegenhain
AU  - Davis J. MacCarthy
AU  - Adrian Alvarez
AU  - Eduard Batlle
AU  - Sagar
AU  - Dominic Grün
AU  - Julia K. Lau
AU  - Stéphane C. Boutet
AU  - Chad Sanada
AU  - Aik Ooi
AU  - Robert C. Jones
AU  - Kelly Kaihara
AU  - Chris Brampton
AU  - Yasha Talaga
AU  - Yohei Sasagawa
AU  - Kaori Tanaka
AU  - Tetsutaro Hayashi
AU  - Itoshi Nikaido
AU  - Cornelius Fischer
AU  - Sascha Sauer
AU  - Timo Trefzer
AU  - Christian Conrad
AU  - Xian Adiconis
AU  - Lan T. Nguyen
AU  - Aviv Regev
AU  - Joshua Z. Levin
AU  - Swati Parekh
AU  - Aleksandar Janjic
AU  - Lucas E. Wange
AU  - Johannes W. Bagnoli
AU  - Wolfgang Enard
AU  - Marta Gut
AU  - Rickard Sandberg
AU  - Ivo Gut
AU  - Oliver Stegle
AU  - Holger Heyn
TI  - Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
AID  - 10.1101/630087
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 630087
4099  - http://biorxiv.org/content/early/2019/05/13/630087.short
4100  - http://biorxiv.org/content/early/2019/05/13/630087.full
AB  - Single-cell RNA sequencing (scRNA-seq) is the leading technique for charting the molecular properties of individual cells. The latest methods are scalable to thousands of cells, enabling in-depth characterization of sample composition without prior knowledge. However, there are important differences between scRNA-seq techniques, and it remains unclear which are the most suitable protocols for drawing cell atlases of tissues, organs and organisms. We have generated benchmark datasets to systematically evaluate techniques in terms of their power to comprehensively describe cell types and states. We performed a multi-center study comparing 13 commonly used single-cell and single-nucleus RNA-seq protocols using a highly heterogeneous reference sample resource. Comparative and integrative analysis at cell type and state level revealed marked differences in protocol performance, highlighting a series of key features for cell atlas projects. These should be considered when defining guidelines and standards for international consortia, such as the Human Cell Atlas project.