From: Effect of invasive mechanical ventilation on the diversity of the pulmonary microbiota
Species | Age | Gender | Study design | Samples | Sequencing platform | Transcriptionally distinct cell clusters | Immune-relevant events due to changed O2 concentration exclusively | Study |
---|---|---|---|---|---|---|---|---|
Mice (C57BL/6) | Postnatal day (P) 0 | Random | Normoxia or hyperoxia (85% O2) for 3Â days (P3), 7Â days (P7), or 14Â days (P14), and subsequent lung cell preparation for scRNA-seq; 6 mice per group, 36 in total | Whole lung | NextSeq500 (Illumina) | 34 clusters | The study described cell cluster- /cell type-specific transcriptional analysis in response to hyperoxia, compared to normoxia (via gene set enrichment analysis (GSEA)) | Hurskainen et al. [76] |
Mice (C57BL/6 J) | Postnatal day (P) 0 | Random | Normoxia or hyperoxia (> 95% O2) for 3 days, and lung cell preparation for scRNA-seq on P7 and P60 | Whole lung | HiSeq (Illumina) | 45 clusters | The study did not analyze the cell cluster-/cell type-specific transcriptional analysis in response to hyperoxia, compared to normoxia | Scaffa et al. [77] |
Mice (C57BL/6 J) | 8–10 weeks | Male | 12 h:12 h light/dark cycle for 2 weeks, then intermittent hypoxia (6%, ~ 30 hypoxic events/h; n = 3) or normoxia (n = 3) for 9 days, then scRNA-seq next day | Whole lung | HiSeq 2500 (Illumina) | 25 clusters | The study described cell cluster- /cell type-specific transcriptional analysis in response to hypoxia, compared to normoxia (via biological process enrichment analysis in the DAVID database) | Wu et al. [80] |
Mice (CDH5-CreERT2-ROSA26-TdTomato, endothelial cell-specific Cdh5-driven expression of Td Tomato red fluorescent protein) | NA | Female | Gavaging tamoxifen for TdTomato induction. Then hypoxia (10% O2 for 3 weeks)/weekly subcutaneous injection of 20 mg/kg Sugen 5416 (n = 3), or normoxia for 3 weeks. Then sorting TdTomato + mouse lung cells for scRNA-seq | TdTomato + mouse lung cells (endothelial cells) | NovaSeq S2 (Illumina) | 8 clusters | Due to the injection of Sugen 5416 in hypoxia group (not in normoxia group), so the study design could not provide hypoxia-exclusive effect on endothelial cells | Rodor et al. [79] |
Rats (Sprague–Dawley) | Adult (250 g–350 g) | Male | Subcutaneous injection of 20 mg/kg Sugen 5416 followed with 10% O2 for 21 days and the normoxia for 14 days (n = 6); Normoxia control were kept for 28 days (n = 6) | Whole lung | HiSeq 4000 (Illumina) | 28 clusters | Due to the injection of Sugen 5416 in hypoxia group (not in normoxia group), so the study design could not provide hypoxia-exclusive effect on lung cells | Hong et al. [78] |