多个物种的肾脏部位巨噬细胞比较

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最近在单细胞天地公众号看到了：多个组织的成纤维细胞图谱 的介绍，挺有意思的， 这样的思路完全可以任意扩展开来啊，多个组织的多种细胞亚群都是可以比较，甚至迁移到多个物种啊，如果多物种的单细胞数据集存在的话！

然后我确实搜索了一下， 这样的研究已经是很多了，比如多个物种的肾脏部位巨噬细胞比较，发表它的文章J Am Soc Nephrol. 2019 May;标题是：《Single-Cell RNA Sequencing Identifies Candidate Renal Resident Macrophage Gene Expression Signatures across Species》，测序数据是公开可以获取的，GSE128993. 这个研究跨越四个物种，如下所示：

GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL20084 Illumina NextSeq 500 (Rattus norvegicus)
GPL20983 Illumina NextSeq 500 (Sus scrofa)

而且还采纳了两个主流单细胞测序技术平台：

GSE128991 Identification of renal resident macrophages across species [C1]
GSE128992 Identification of renal resident macrophages across species [10X]

给出来的表达矩阵文件似乎是有点小：

GSM3689774_human_10X_matrix.txt.gz 3.9 Mb
GSM3689775_pig_10X_matrix.txt.gz 6.2 Mb
GSM3689776_mouse_10X_matrix.txt.gz 4.1 Mb
GSM3689777_rat_10X_matrix.txt.gz 5.5 Mb

大家可能是需要首先下载每个文件，独立走单细胞的降维聚类分群流程，因为不同物种的基因名字不一样哦。因为都是肾脏部位巨噬细胞，所以理论上标记基因是有一定程度的保守性的啦。

文章里面主要的关于单细胞转录组数据层面的描述：

  • We sorted populations of immune cells (CD45+) from the kidney, excluded lymphoid cells, and subjected the remaining cells to scRNAseq using the 10× Genomics platform (Figure 1A).
  • For this analysis, we excluded cells from both the T cell (CD3e in mouse and pig, CD3 in rat and human) and B cell lineage (B220 in mouse, CD45RA in rat, CD19 in human) using fluorescence-labeled antibodies that were commercially available.
  • Using this approach, we analyzed 3013, 3935, 4671, and 2868 single cells from mouse, rat, pig, and human kidney tissue, respectively (Supplemental Table 1).
  • The mean reads per cell were 80,508, 54,456, 61,638, and 112,080 for mouse, rat, pig, and human cells, respectively.
  • Unbiased hierarchical clustering and heatmap analysis using Seurat shows a unique innate immune cell landscape in each species with each color representing a different cell population (Figure 1, B and C).

附件信息非常详实：

  • Supplemental Table 1. Number of cells, genes, and reads in single-cell data from mouse, rat, pig, and human kidneys.
  • Supplemental Table 2. Top DEGs in mouse innate immune cell populations.
  • Supplemental Table 3. Number of reads in individual cells from mouse Fluidigm C1 scRNAseq data.
  • Supplemental Figure 1. scRNAseq reveals the presence of CD79a+ B cells in mouse kidney tissue.
  • Supplemental Figure 2. Gating strategy used in Fluidigm C1 studies to identify infiltrating and resident macrophages on the basis of canonical markers.
  • Supplemental Figure 3. scRNAseq reveals the presence of distinct clusters of innate immune cells in rat kidney tissue.
  • Supplemental Figure 4. scRNAseq reveals the presence of distinct clusters of innate immune cells in pig kidney tissue.
  • Supplemental Figure 5. scRNAseq reveals the presence of distinct clusters of innate immune cells in human kidney tissue.
  • Supplemental Figure 6. Fluidigm C1 scRNAseq of single cells from human kidney tissue.
  • Supplemental Figure 7. Gating strategy used to identify candidate resident macrophages on the basis of novel markers.
  • Supplemental Figure 8. Chimerism of blood-derived cells in mouse parabiosis studies.

是一篇很不错的数据分析范文！

同样的道理，是不是可以做脑部区域的巨噬细胞（小胶质细胞）的跨物种比较呢？或者，T细胞，B细胞？

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