Closed ixxmu closed 2 years ago
分享是一种态度
文章题目:CancerSCEM: a database of single-cell expression map across various human cancers
日期:2021-09-29
期刊:Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gkab905
一个包含人类多种癌症的scRNA数据库CancerSCEM,除了常规的分析之外,还提供网站可视化和在线分析(https://ngdc.cncb.ac.cn/cancerscem)
所以,CancerSCEM (Cancer Single-cell Ex- pression Map) 提供了数据搜集、整理、分析、可视化一体。目前包括人类20种癌症的208个样本的638,341个单细胞数据
数据来自:GEO、ArrayExpress、EBI、GSA、ZENODO,涵盖了10X Genomics, Smart-seq2, Drop-seq, Seq-Well and Microwell 5大平台,其中原始数据占比82.69%。
PCA + tSNE + UMAP 聚类
biomarker 基因来自Cell Marker数据库,细胞注释三步走:
scCancer v2.2.0 + Copy- KAT v1.0.4:copy number variation assessment
A group of marker genes, such as EPCAM, KRT8, KRT18, KRT19 and EGFR in glioblastoma cells that represent cancer cells or cancer stem cells, were investi- gated in parallel.
Cells with significantly abnormal CNV levels and high expression levels of above marker genes were defined as malignant cells
Manual annotation :自己看marker基因表达
常见的比如:T cells (e.g. CD3D, CD3E), B cells (e.g. MS4A1, BANK1), Macrophages/Monocytes (e.g. CD68, CD14), Mast cells (e.g. SLC18A2, ASIC4), Endothelial cells (e.g. VWF, PECAM1), Fibroblasts (e.g. FAP, NECTIN1), Oligoden- drocytes (e.g. OLIG1, PLP1) and Astrocytes (e.g. SLC1A3, GFAP)
网站的Documents也给出了所使用的全部marker基因列表
SingleR: 工具注释
此外,还将T、B细胞继续进行细分亚群,最终得到了包括免疫细胞在内的33种细胞类型
FindMarkers用来对每个细胞群进行差异分析
如果你对单细胞转录组研究感兴趣,但又不知道如何入门,也许你可以关注一下下面的课程
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https://mp.weixin.qq.com/s/3DlLp7xeQKR9WFmjTI0AbA