小鼠的肿瘤免疫微环境推断可以用seq-ImmuCC

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最近检查自己的谷歌Gmail邮箱，发现它推送了我感兴趣的一个教授的文章《A Spontaneous Aggressive ERa+ Mammary Tumor Model Is Driven by Kras Activation》，里面提到了小鼠的肿瘤免疫微环境的推断。这个教授就是biostar论坛的创始人，其 lab 链接是：https://griffithlab.org/team/

image-20201029122356029
文章链接是：https://www.cell.com/cell-reports/pdfExtended/S2211-1247(19)30884-8 ，研究者自己的数据只有430.18 Gb，包括基因组数据和转录组数据，链接是： https://www.ncbi.nlm.nih.gov/bioproject/PRJNA489661/ 样本量并不大，但是分析很出彩。

转录组测序数据介绍

Mammary cell preparations (MCPs) were harvested from the caudal glands of NRL-PRL females (n = 5) at 12 weeks (young adults), prior to morphologic evidence of pathology.
Following the formation of spontaneous tumors at 15–20 months of age, three tissues from these mice were collected:

  • (1) end-stage mammary tumors,
  • (2) adjacent non-tumor mammary tissue (aged mammary glands [AMGs]),
  • (3) matched tail tissue
    可以看到是5只小鼠，共15个样品：
    描述是：(C) seq-ImmuCC was used to predict the relative proportions of immune cell populations (y axis) in MCPs, AMGs, and end-stage tumors from the discovery set. Samples are ordered by identifier (MCP A–E, AMG 1–5, and Tumors 1–5).
    肿瘤免疫微环境推断
    就是这个文章，让我注意的了seq-ImmuCC这个软件工具，因为太多粉丝留言问到了小鼠转录组测序数据如何推断肿瘤微环境的各种免疫细胞比例。这就是答案！

    另外推荐一个数据库CellKb

    Announcing our latest offering, CellKb Immune - a database of 1,521 marker gene sets of 180 immune cell types from mouse collected from 130 publications.链接：https://www.cellkb.com/immune
    免疫细胞相关基因的集大成者！
    image-20201127120754480

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