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Table 2 Related studies on changes in the local immune microenvironment of the lung due to O2 concentration perturbation based on scRNA-seq technique, which in turn affects the diversity of the pulmonary microbiota

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 3 days (P3), 7 days (P7), or 14 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]