Single-cell sequencing data analysis

YC Yunlong Cao
AY Ayijiang Yisimayi
YB Yali Bai
WH Weijin Huang
XL Xiaofeng Li
ZZ Zhiying Zhang
TY Tianjiao Yuan
RA Ran An
JW Jing Wang
TX Tianhe Xiao
SD Shuo Du
WM Wenping Ma
LS Liyang Song
YL Yongzheng Li
XL Xiang Li
WS Weiliang Song
JW Jiajing Wu
SL Shuo Liu
XL Xuemei Li
YZ Yonghong Zhang
BS Bin Su
XG Xianghua Guo
YW Yangyang Wei
CG Chuanping Gao
NZ Nana Zhang
YZ Yifei Zhang
YD Yang Dou
XX Xiaoyu Xu
RS Rui Shi
BL Bai Lu
RJ Ronghua Jin
YM Yingmin Ma
CQ Chengfeng Qin
YW Youchun Wang
YF Yingmei Feng
JX Junyu Xiao
XX Xiaoliang Sunney Xie
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The raw fastq files of single-cell gene expression, feature barcode, and VDJ sequencing were processed using the multi pipeline of 10X Genomics’ Cell Ranger (5.0.0) software with GRCh38 reference genome (Cell Ranger GRCh38 Reference — 5.0.0). The output filtered feature-barcode matrices were input to R software (v3.6.2) with Seurat package (v3.2.0) for downstream analysis.37 Cells with < 300 or > 9000 genes, < 500 or > 50,000 UMIs, or > 10% mitochondrial UMIs were filtered out. Cell types were identified using SingleR package with “MonacoImmuneData” as reference.38,39

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