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.
Researchers at the Wellcome Sanger Institute assess the effect of cold storage on fresh healthy spleen, esophagus, and lung from ≥ 5 donors over 72 h. They collected 240,000 high-quality single-cell transcriptomes with detailed cell type annotations and whole genome sequences of donors, enabling future eQTL studies. These data provide a valuable resource for the study of these 3 organs and will allow cross-organ comparison of cell types. The researchers saw 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, they observed 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.
Loss of data quality is associated with increased “ambient RNA” and “debris” reads in the data
a Average spread of normalized UMI counts per droplet in the spleen, which were classified into ambient RNA, debris, and cellular material. b Mean values of normalized UMI in droplets containing debris or c cellular material. Individual sample means are shown for each donor with corresponding shape; color represents tissue. Means across donors per time point are shown by filled circles; whiskers represent standard deviation. p values were gained by Student’s paired (T0 vs 72 h) and non-paired (T0 vs 24 h) t test