scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
E. Madissoon, A. Wilbrey-Clark, R. J. Miragaia, K. Saeb-Parsy, K. T. Mahbubani, N. Georgakopoulos, P. Harding, K. Polanski, N. Huang, K. Nowicki-Osuch, R. C. Fitzgerald, K. W. Loudon, J. R. Ferdinand, M. R. Clatworthy, A. Tsingene, S. van Dongen, M. Dabrowska, M. Patel, M. J. T. Stubbington, S. A. Teichmann, O. Stegle, K. B. Meyer
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.
Datasets
1. Spleen
Metadata
donor_id
Time
donor_time
organ
sample
leiden
assay_ontology_term_id
cell_type_ontology_term_id
development_stage_ontology_term_id
disease_ontology_term_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sex_ontology_term_id
tissue_ontology_term_id
author_cell_type
suspension_type
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
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HCATisStab758720323225 cells HCATisStabAug17727639416290 cells HCATisStab75872097358 cells HCATisStab75872006438 cells HCATisStab74638494727 cells HCATisStabAug1772763914018 cells HCATisStab74638463600 cells HCATisStab74638473510 cells HCATisStab74638483484 cells HCATisStabAug1772763923450 cells HCATisStab75872063390 cells HCATisStabAug1773765632569 cells HCATisStabAug1770780162064 cells HCATisStabAug1770780182059 cells HCATisStabAug1773765611903 cells HCATisStabAug1770780191810 cells HCATisStabAug1773765651772 cells HCATisStabAug1770780171407 cells HCATisStabAug1773765671182 cells HsapDv:000023971595 cells HsapDv:000023715321 cells NCBITaxon:960694256 cells UBERON:000210694256 cells T_CD8_activated5009 cells follicular B cell16286 cells natural killer cell14458 cells CD4-positive, alpha-beta T cell11081 cells activated CD8-positive, alpha-beta T cell5009 cells CD8-positive, alpha-beta T cell3510 cells naive thymus-derived CD4-positive, alpha-beta T cell3224 cells T follicular helper cell2737 cells IgM plasma cell2488 cells IgG plasma cell1799 cells CD8-alpha alpha positive, gamma-delta intraepithelial T cell1620 cells CD4-positive, CD25-positive, alpha-beta regulatory T cell1010 cells innate lymphoid cell566 cells plasmacytoid dendritic cell256 cells conventional dendritic cell239 cells hematopoietic stem cell164 cells fifth decade human stage71595 cells third decade human stage15321 cells sixth decade human stage7340 cells 2. Esophagus Epithelium
Metadata
donor_id
Time
donor_time
organ
sample
leiden
assay_ontology_term_id
cell_type_ontology_term_id
development_stage_ontology_term_id
disease_ontology_term_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sex_ontology_term_id
tissue_ontology_term_id
author_cell_type
suspension_type
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
HCATisStab74136218749 cells HCATisStabAug1771848628019 cells HCATisStab74136227206 cells HCATisStab76460306534 cells HCATisStab76460284773 cells HCATisStab76460294579 cells HCATisStab76190654159 cells HCATisStab74136203819 cells HCATisStabAug1773765683780 cells HCATisStab76190643771 cells HCATisStabAug1773765623728 cells HCATisStabAug1773765663418 cells HCATisStab74136193385 cells HCATisStabAug1773765643381 cells HCATisStab75872012900 cells HCATisStab76190672800 cells HCATisStabAug1771848632670 cells HCATisStab75872072235 cells HCATisStab75872042057 cells HCATisStab76460311838 cells HCATisStab75872101668 cells HCATisStab76190661437 cells HCATisStabAug1771848581041 cells HsapDv:000024129891 cells HsapDv:000023923167 cells HsapDv:000024023159 cells HsapDv:000023811730 cells NCBITaxon:960687947 cells UBERON:000197687947 cells Epi_stratified50469 cells Epi_suprabasal10000 cells NK_T_CD8_Cytotoxic201 cells stratified epithelial cell50469 cells epithelial cell30195 cells blood vessel endothelial cell1498 cells CD4-positive, alpha-beta T cell1350 cells CD8-positive, alpha-beta T cell797 cells epithelial cell of stratum germinativum of esophagus754 cells mononuclear phagocyte334 cells CD8-positive, alpha-beta cytotoxic T cell201 cells endothelial cell of lymphatic vessel105 cells mucus secreting cell55 cells epithelium of esophagus87947 cells seventh decade human stage29891 cells fifth decade human stage23167 cells sixth decade human stage23159 cells fourth decade human stage11730 cells 3. Lung Parenchyma
Metadata
donor_id
Time
donor_time
leiden
sample
assay_ontology_term_id
cell_type_ontology_term_id
development_stage_ontology_term_id
disease_ontology_term_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sex_ontology_term_id
tissue_ontology_term_id
author_cell_type
suspension_type
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
HCATisStab77471985110 cells HCATisStab76460334361 cells HCATisStab76460324252 cells HCATisStab75872023772 cells HCATisStab75097363718 cells HCATisStab75872083689 cells HCATisStab77471973580 cells HCATisStab75872053471 cells HCATisStab77472003445 cells HCATisStab76599693299 cells HCATisStab76460353037 cells HCATisStab77471992703 cells HCATisStab75872112631 cells HCATisStab75097342347 cells HCATisStab76599702050 cells HCATisStab75097351918 cells HCATisStab76460341713 cells HCATisStab76599711418 cells HCATisStab7659968505 cells HsapDv:000024128201 cells HsapDv:000023913563 cells NCBITaxon:960657019 cells UBERON:000894657019 cells Macrophage_MARCOpos4512 cells Macrophage_MARCOneg937 cells DC_Monocyte_Dividing242 cells Macrophage_Dividing94 cells natural killer cell10548 cells CD4-positive, alpha-beta T cell7211 cells CD8-positive, alpha-beta cytotoxic T cell5755 cells lung macrophage5543 cells blood vessel endothelial cell2694 cells regulatory T cell481 cells lung ciliated cell466 cells endothelial cell of lymphatic vessel337 cells mononuclear cell242 cells conventional dendritic cell163 cells plasmacytoid dendritic cell46 cells lung parenchyma57019 cells seventh decade human stage28201 cells fifth decade human stage13563 cells eighth decade human stage7983 cells sixth decade human stage7272 cells Analyze this study
Source data
https://cellxgene.cziscience.com/collections/4d74781b-8186-4c9a-b659-ff4dc4601d91
Alias names
PRJEB31843, E-HCAD-1, PMID31892341, PMC6937944
Cite this study
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. and Fitzgerald, R.C., 2020. scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation. Genome biology, 21, pp.1-16. https://doi.org/10.1186/s13059-019-1906-x
