ArticleGenome biology2019
scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 194 papers, 1 of them a synthesis that pooled it.
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Who cites it
194 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.Nature medicine · 2021Pooled it
- Immunomic longitudinal profiling of the NeoPembrOv trial identifies drivers of immunoresistance in high-grade ovarian carcinoma.Nature communications · 2024Trial
- celltypeEnrich: a consensus-based scRNA-seq cluster annotation tool.bioRxiv : the preprint server for biology · 2026Article
- BMI-genome interactions regulate global gene expression with emphasis in brain and gut.Cell genomics · 2026Article
- scDifformer: diffusion-based post-training for virtual cell modeling across large-scale single-cell data.Nucleic acids research · 2026Article
- Interpretable deep generative ensemble learning for single-cell omics with Hydra.Molecular systems biology · 2026Article
- Cell-Type Deconvolution of Equine BALF RNA-Seq: A Critical Comparison with Matched Single-Cell Data.Genes · 2026Article
- ProtoCloud: A prototypical self-explaining model for single-cell analysis.Cell genomics · 2026Article
- Spatiotemporal Transcriptomic Dissection Uncovers Age-Dependent Deceleration of Esophageal Cell Differentiation.bioRxiv : the preprint server for biology · 2026Article
- Age- and tissue-dependent diversity of human plasmacytoid dendritic cells uncovers a cycling subset dominant in early life and cancer.Immunity · 2026Article
- Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.Molecular diagnosis & therapy · 2026Review
- Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq.Nature communications · 2026Article
- Genotype-to-Phenotype Mapping of Somatic Clonal Mosaicism via Single-Cell Co-Capture of DNA Mutations and mRNA Transcripts.Cancer discovery · 2026Article
- A single-cell immune atlas of primary and secondary lymphoid organs in pigs.Frontiers in immunology · 2026Article
- Article
- hECA v2.0: an AI-ready ensemble cell atlas of single-cell RNA and ATAC sequencing data.Scientific data · 2025Article
- Deciphering precursor cell dynamics in esophageal preneoplasia via genetic barcoding and single-cell transcriptomics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Optimal marker genes forGenome research · 2025Article
- USPPAR is a cost-effective, scalable, and highly sensitive single-cell RNA sequencing workflow compatible with diverse specimens.PLoS biology · 2025Article
- Concerted changes in Epithelium and Stroma: a multi-scale, multi-omics analysis of progression from Barrett's Esophagus to adenocarcinoma.Developmental cell · 2025Article
134 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
22 authors.
Funding
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.
resultsThis 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.
conclusionsIn 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.