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Kraus, G.* ; Weigelt, M.* ; Reinhardt, S.* ; Petzold, A.* ; Dahl, A.* ; Bonifacio, E.

Reproducibility of 10x Genomics single cell RNA sequencing method in the immune cell environment.

J. Immunol. Methods 502:113227 (2022)

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Open Access Green as soon as Postprint is submitted to ZB.

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10x Genomics is a highly accessible single cell RNA sequencing platform that allows for simultaneous gene expression analysis and identification of receptor chain combinations in cells of the adaptive immune system. Here, we asked whether the gene and receptor expression measurements in peripheral blood mononuclear cells (PBMC) are influenced by technical, cell freezing, FACS-processing, and day to day biological variation. No differentially expressed gene was observed between 1. triplicates aliquots taken from the same vial of frozen PBMC; 2. triplicate vials of frozen PBMC; and 3. triplicate aliquots taken from the same vial of frozen PBMC and processed separately for FACS staining and sorting of different PBMC populations. A small number of differentially expressed genes were observed between PBMC sampled, isolated and frozen from the same donor on different days, and these differences were more pronounced in the memory B cells than other cell populations. T cell receptors were recovered in all replicates when at least 5 cells per clonotype were identified. These findings show high reproducibility of 10x Genomics single cell RNA sequencing data in the immune cell context.

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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords 10x Genomics ; Gene-expression Analysis ; Peripheral Blood Mononuclear Cells (pbmc) ; Reproducibility ; Single-cell ; T Cell Receptor (tcr)

ISSN (print) / ISBN 0022-1759

e-ISSN 1872-7905

Journal Journal of Immunological Methods

Quellenangaben Volume: 502, Article Number: 113227

Publisher Elsevier

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) Institute of Diabetes and Obesity (IDO)
Institute for Pancreatic Beta Cell Research (IPI)

Grants Innovative Medicines Initiative
Juvenile Diabetes Research Foundation United States of America