项目编号

PRJCA016296

项目标题

Single-cell RNA-seq of peripheral blood mono nuclear cells (PBMCs) from 26 donors and 5 NSCLC cell lines

涉及领域

Medical

数据类型

Single cell sequencing

物种名称

Homo sapiens

描述信息

Single-cell RNA-seq (scRNA-seq) analysis of multiple samples separately is expensive and may cause batch effect. Multiplexing several samples for one experiment using exogenous barcodes or demultiplexing scRNA-seq data based on genome-wide RNA mutations is experimentally or computationally challenging and scale-limited, respectively. Mitochondria is a smaller genome set that can provide concise information for individual genotypes. In this study, we developed a computational algorithm "mitoSpliter" that enables sample demultiplexing based on somatic mutations in mitochondrial RNA (mtRNA). We demonstrated that mtRNA variants are computationally capable of demultiplexing large-scale scRNA-seq data. The analysis of peripheral blood mononuclear cells (PBMCs) revealed that mitoSpliter can accurately analyze up to 10 samples and 60K cells in a single experiment in ~6 hours on affordable computational resources. Further application of mitoSpliter to non-small cell lung cancer (NSCLC) cells uncovered the synthetic lethality of TOP2A inhibition and BET chemical degradation in the BET inhibitor-resistant cells, indicating that mitoSpliter will accelerate the application of scRNA-seq assay in biomedical research.

样品范围

Single cell

发布日期

2023-04-17

项目资金来源

机构	项目类型	授权项目ID	授权项目名称
Ministry of Science and Technology of the People's Republic of China (MOST)		2020YFA0803601
Ministry of Science and Technology of the People's Republic of China (MOST)		2018YFA0801300
National Natural Science Foundation of China (NSFC)		32071138
State Key Laboratory of Genetic Engineering		SKLGE-2118
National Natural Science Foundation of China (NSFC)		22104080
National Natural Science Foundation of China (NSFC)		21735004
National Natural Science Foundation of China (NSFC)		21927806
Innovative research team of high-level local universities in Shanghai		SHSMU-ZLCX20212601

提交者

Xinrui Lin (linxinrui@renji.com)

提交单位

Shanghai Jiaotong University School of Medicine

提交日期

2023-04-17

项目包含数据信息

资源名称	描述
BioSample (35) show	-
SAMC2702433	scRNA-seq of mixture of NSCLS 5 cell lines: control treatment
SAMC2702429	scRNA-seq of mixture of NSCLS 5 cell lines: drug treatment
SAMC2702426	scRNA-seq of HCC827 cell line: control treatment
SAMC2702421	scRNA-seq of H838 cell line: control treatment
SAMC2702418	scRNA-seq of H2228 cell line: control treatment
SAMC2702414	scRNA-seq of H1975 cell line: control treatment
SAMC2702410	scRNA-seq of A549 cell line: control treatment
SAMC2702407	scRNA-seq of mixture of 10 donors: PBMCs
SAMC2702403	scRNA-seq of mixture of 5 donors: B408-B412 PBMCs
SAMC2702399	scRNA-seq of human: PBMCs
SAMC2702396	scRNA-seq of human: PBMCs
SAMC2702389	scRNA-seq of human: PBMCs
SAMC2702385	scRNA-seq of human: PBMCs
SAMC2702382	scRNA-seq of human: PBMCs
SAMC2702378	scRNA-seq of human: PBMCs
SAMC2702374	scRNA-seq of human: PBMCs
SAMC2702367	scRNA-seq of human: PBMCs
SAMC2702364	scRNA-seq of human: PBMCs
SAMC2702358	scRNA-seq of human: PBMCs
SAMC2702354	scRNA-seq of human: PBMCs
SAMC2702351	scRNA-seq of human: PBMCs
SAMC2702346	scRNA-seq of human: PBMCs
SAMC2702342	scRNA-seq of human: PBMCs
SAMC2702338	scRNA-seq of human: PBMCs
SAMC2702335	scRNA-seq of human: PBMCs
SAMC2702331	scRNA-seq of human: PBMCs
SAMC2702327	scRNA-seq of human: PBMCs
SAMC2702323	scRNA-seq of human: PBMCs
SAMC2702318	scRNA-seq of human: PBMCs
SAMC2702314	scRNA-seq of human: PBMCs
SAMC2702311	scRNA-seq of human: PBMCs
SAMC2702307	scRNA-seq of human: PBMCs
SAMC2702304	scRNA-seq of human: PBMCs
SAMC2702299	scRNA-seq of human: PBMCs
SAMC2702297	scRNA-seq of human: PBMCs