Lung, spleen and oesophagus tissue remains stable for scRNAseq in cold preservation

Abstract

BackgroundThe 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. Despite this, there has not yet been a systematic assessment of the effect of cold storage time on the quality of scRNAseq ResultsThis study assessed the effect of cold storage on fresh healthy spleen, oesophagus and lung from ≥5 donors over 72 hours. We collected 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 three organs and will allow cross-organ comparison of cell types.We see little effect of cold ischaemic time on cell viability, yield, total number of reads per cell and other quality control metrics in any of the tissues within the first 24 hours. However, we observed higher percentage of mitochondrial reads, indicative of cellular stress, and

Quantitative and molecular differences distinguish adult human medullary and extramedullary haematopoietic stem and progenitor cell landscapes

“…We thus infer that our analysis is overall reflective of steady-state conditions in humans. Nonetheless we cannot exclude that some of the molecular features and/or the generally poised state observed here and discussed below are influenced by cellular responses induced upon death and/or tissue storage (Madissoon et al, 2019).…”

Sampling artifacts in single-cell genomics cohort studies

“…Finally, we hypothesized that cold sample storage could prevent time-related sampling effects by minimizing active and passive cell responses. In line, tissues (lung, pancreas and oesophagus) preserved at cold temperatures (4°C) did not show altered single-cell gene expression profiles or cell type composition changes up to 72 hours of storage 15 . Importantly, changing storage temperatures could be readily implemented in prospective cohort study designs to enable subsequent scRNA-seq.…”

Prediction of SARS-CoV interaction with host proteins during lung aging reveals a potential role for TRIB3 in COVID-19

“…We analyzed the expression of TRIB3, HAPLN2, and ACE2, in different lung cell populations by using two previously published human single-cell RNA-seq data (Table S4) 19,20 . The first dataset 20 was explored in the UCSC Cell Browser (http://nupulmonary.org/resources/), aiming the identification of the cell populations expressing those genes.…”

“…The samples with pulmonary fibrosis presented in this dataset were omitted from our analysis, and only non-diseased lung samples were included (n=8). We further used an independent single-cell RNA-seq dataset 19 (n=5), available at the Human Cell Atlas Portal (https://data.humancellatlas.org/explore/projects/c4077b3c-5c98-4d26-a614-246d12c2e5d7), to confirm that expression TRIB3 and ACE2 are expressed in alveolar epithelial cells (types 1 and 2) and in ciliate cells. Access in March 2020.…”

“…The reanalysis of lung single-cell RNA sequencing data 19,20 demonstrated TRIB3 expressed mainly in alveolar type I (AT1) and type II (AT2) cells and in ciliated cells ( Figure 1d-f, Figure S3), which also express SARS-CoV-2 receptor ACE2 7,8,21 . The involvement of TRIB3 in viral infection is poorly understood; however, its inhibition was associated with an increase of hepatitis C virus (HCV) replication 22 .…”