scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulti...

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Bibliographic Details
Published in:	Genome Biology Vol. 21; no. 1; p. 1
Main Authors:	Madissoon, E, Wilbrey-Clark, A, Miragaia, R J, Saeb-Parsy, K, Mahbubani, K T, Georgakopoulos, N, Harding, P, Polanski, K, Huang, N, Nowicki-Osuch, K, Fitzgerald, R C, Loudon, K W, Ferdinand, J R, Clatworthy, M R, Tsingene, A, van Dongen, S, Dabrowska, M, Patel, M, Stubbington, M J T, Teichmann, S A, Stegle, O, Meyer, K B
Format:	Journal Article
Language:	English
Published:	England BioMed Central 31-12-2019 BMC
Subjects:	Biopsy Cold Temperature Contamination Cryopreservation Esophagus Esophagus - cytology Gene expression Genomes Genomics Human Humans Ischemia Ischemic time Kidneys Laboratories Lung Lung - cytology Lymphocytes T Mitochondria Quality Quality control Refrigeration Ribonucleic acid RNA Sequence Analysis, RNA Single-Cell Analysis Single-cell RNA sequencing Spleen Spleen - cytology Tissue Preservation - methods Human Spleen Ischemic time Single-cell RNA sequencing Lung Esophagus
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Summary:	The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design. This study assesses the effect of cold storage on fresh healthy spleen, esophagus, and lung from ≥ 5 donors over 72 h. We collect 240,000 high-quality single-cell transcriptomes with detailed cell type annotations and whole genome sequences of donors, enabling future eQTL studies. Our data provide a valuable resource for the study of these 3 organs and will allow cross-organ comparison of cell types. We see little effect of cold ischemic time on cell yield, total number of reads per cell, and other quality control metrics in any of the tissues within the first 24 h. However, we observe a decrease in the proportions of lung T cells at 72 h, higher percentage of mitochondrial reads, and increased contamination by background ambient RNA reads in the 72-h samples in the spleen, which is cell type specific. In conclusion, we present robust protocols for tissue preservation for up to 24 h prior to scRNA-seq analysis. This greatly facilitates the logistics of sample collection for Human Cell Atlas or clinical studies since it increases the time frames for sample processing.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23
ISSN:	1474-760X 1474-7596 1474-760X
DOI:	10.1186/s13059-019-1906-x