Tissue Type(s): Healthy Lung

Contributed by: Kerstin Meyer, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK

Manuscript: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells (https://www.biorxiv.org/content/10.1101/2020.04.19.049254v1)

Description: This study allows one to visualize and query genes as well as explore cell types, technical batches, and cell metrics associated with the manuscript. If published, this version of the data set is focused on the manuscript and is a subset of what may be made available by the original manuscript.

Original Publication: Madissoon, E., et al. "scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation." Genome Biology 21.1 (2020): 1-16.

Full dataset: The datasets generated for this study are available through the Human Cell Atlas Data Coordination Platform and NCBI BIOPROJECT accession code PRJEB31843 (https://prod.data.humancellatlas.org/explore/projects/c4077b3c-5c98-4d26-a614-246d12c2e5d7). Relevant processed data is shared here in the downloads tab.

Abstract: 

Background

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.

Results

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.

Conclusions

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.