標(biāo)題： Single-cell RNA landscape of intratumoral heterogeneity and immunosuppressive microenvironment in advanced osteosarcoma
DOI： https://doi.org/10.1038/s41467-020-20059-6
雜志： nature communications
發(fā)布年份：2020
數(shù)據(jù)集：GSE152048
打開(kāi)數(shù)據(jù)集地址：https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152048
可以看到關(guān)于數(shù)據(jù)集的基本信息：
下載supplementary file：
下載完成的文件：
解壓后：
11個(gè)文件夾對(duì)應(yīng)11個(gè)病人，每個(gè)文件夾都有barcodes,features,matrix三個(gè)gz壓縮文件。
使用R讀入數(shù)據(jù)，代碼來(lái)自公眾號(hào)【生信技能樹(shù)】
rm(list = ls())
setwd('~/projects/GSE152048/')
library(Seurat)
#指定數(shù)據(jù)存放位置
samples=list.files("./GSE152048_RAW/outputs/")
samples
# [1] "BC10" "BC11" "BC16" "BC17" "BC2" "BC20" "BC21" "BC22" "BC3" "BC5" "BC6"
dir <- file.path('./GSE152048_RAW/outputs/',samples)
names(dir) <- samples
#讀取數(shù)據(jù)創(chuàng)建Seurat對(duì)象
counts <- Read10X(data.dir = dir)
dim(counts)
[1] 32864 130761
sce.all = CreateSeuratObject(counts,
min.cells = 5,
min.features = 300 )
dim(sce.all) #查看基因數(shù)和細(xì)胞總數(shù)
#[1] 25730 129755
# as.data.frame(sce.all@assays$RNA$counts[1:10, 1:2])
table(sce.all@meta.data$orig.ident) #查看每個(gè)樣本的細(xì)胞數(shù)
# BC10 BC11 BC16 BC17 BC2 BC20 BC21 BC22 BC3 BC5 BC6
#17481 13444 10210 4032 5937 11063 6342 9104 8684 21824 21634
head(sce.all@meta.data)
# orig.ident nCount_RNA nFeature_RNA
#BC10_AAACCTGAGACTCGGA-1 BC10 23075 3769
#BC10_AAACCTGAGACTTGAA-1 BC10 1177 678
#BC10_AAACCTGAGCTCCTTC-1 BC10 1011 561
#BC10_AAACCTGAGGAACTGC-1 BC10 10465 2542
#BC10_AAACCTGAGGAGTCTG-1 BC10 1359 605
#BC10_AAACCTGAGGATGGAA-1 BC10 9459 2339
創(chuàng)建一個(gè)txt文件用于保存分組信息：
#讀入分組信息
sample.info <- read.table("sample_info.txt",header=T)
#添加group和Pathological_type
for (i in c(2,3)) {
tp <- sample.info[,i]
names(tp) <- sample.info$sample
samples <- sce.all$orig.ident
add_ <- tp[as.character(samples)]
names(add_) <- colnames(sce.all)
sce.all <- AddMetaData(
object = sce.all,
metadata = add_,
col.name = colnames(sample.info)[i]
)}
colnames(sce.all@meta.data)
# [1] "orig.ident" "nCount_RNA" "nFeature_RNA" "group" "Pathological_type"
head(sce.all@meta.data)
# orig.ident nCount_RNA nFeature_RNA group Pathological_type
#BC10_AAACCTGAGACTCGGA-1 BC10 23075 3769 Metastasis Conventional
#BC10_AAACCTGAGACTTGAA-1 BC10 1177 678 Metastasis Conventional
#BC10_AAACCTGAGCTCCTTC-1 BC10 1011 561 Metastasis Conventional
#BC10_AAACCTGAGGAACTGC-1 BC10 10465 2542 Metastasis Conventional
#BC10_AAACCTGAGGAGTCTG-1 BC10 1359 605 Metastasis Conventional
#BC10_AAACCTGAGGATGGAA-1 BC10 9459 2339 Metastasis Conventional
table(sce.all@meta.data$group)
#Metastasis Primary Recurrent
# 21513 83735 24507
table(sce.all@meta.data$Pathological_type)
#Chondroblastic Conventional Intraosseous
# 24199 99214 6342
#保存sce.all
save(file="./GSE152048.rdata",sce.all)
