多个物种的肾脏部位巨噬细胞比较

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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