Inference of differentiation time for single cell transcriptomes using cell population reference data
文献类型：期刊论文
| 作者 | Sun, Na1; Yu, Xiaoming1; Li, Fang1; Liu, Denghui1; Suo, Shengbao1; Chen, Weiyang1; Green, Christopher D.1; McDermott, Joseph1; Han, Jing-Dong J.1; Yu, Xiaoming2 |
| 刊名 | NATURE COMMUNICATIONS
 |
| 出版日期 | 2017 |
| 卷号 | 8期号:-页码:1856 |
| 关键词 | endoplasmic reticulum stress (ER stress) autophagy unfolded protein response (UPR) chaperone proteostasis protein misfolding calreticulin LC3 LC3-interacting region (LIR motif) |
| ISSN号 | 2041-1723 |
| DOI | 10.1038/s41467-017-01860-2 |
| 文献子类 | Article |
| 英文摘要 | Single-cell RNA sequencing (scRNA-seq) is a powerful method for dissecting intercellular heterogeneity during development. Conventional trajectory analysis provides only a pseudotime of development, and often discards cell-cycle events as confounding factors. Here using matched cell population RNA-seq (cpRNA-seq) as a reference, we developed an "iCpSc" package for integrative analysis of cpRNA-seq and scRNA-seq data. By generating a computational model for reference " biological differentiation time" using cell population data and applying it to single-cell data, we unbiasedly associated cell-cycle checkpoints to the internal molecular timer of single cells. Through inferring a network flow from cpRNA-seq to scRNA-seq data, we predicted a role of M phase in controlling the speed of neural differentiation of mouse embryonic stem cells, and validated it through gene knockout (KO) experiments. By linking temporally matched cpRNA-seq and scRNA-seq data, our approach provides an effective and unbiased approach for identifying developmental trajectory and timing-related regulatory events. |
| 学科主题 | Science & Technology - Other Topics |
| WOS关键词 | EMBRYONIC STEM-CELLS ; LARGE GENE LISTS ; RNA-SEQ ; DIRECTED DIFFERENTIATION ; FATE ; QUANTIFICATION ; PROGRESSION ; PROPENSITY ; PRECURSORS ; PACKAGE |
| 语种 | 英语 |
| WOS记录号 | WOS:000416895200003 |
| 出版者 | NATURE PUBLISHING GROUP |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1171]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Chinese Acad Sci, Collaborat Innovat Ctr Genet & Dev Biol, Max Planck Partner Inst Computat Biol,Key Lab Com, CAS Ctr Excellence Mol Cell Sci,Shanghai Inst Bio, Shanghai 200031, Peoples R China; 2.Tsinghua Univ, Sch Med, Tsinghua Peking Ctr Life Sci, Beijing 100084, Peoples R China; 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, State Key Lab Cell Biol, Shanghai 200031, Peoples R China, |
| 推荐引用方式 GB/T 7714 | Sun, Na,Yu, Xiaoming,Li, Fang,et al. Inference of differentiation time for single cell transcriptomes using cell population reference data[J]. NATURE COMMUNICATIONS,2017,8(-):1856. |
| APA | Sun, Na.,Yu, Xiaoming.,Li, Fang.,Liu, Denghui.,Suo, Shengbao.,...&,.(2017).Inference of differentiation time for single cell transcriptomes using cell population reference data.NATURE COMMUNICATIONS,8(-),1856. |
| MLA | Sun, Na,et al."Inference of differentiation time for single cell transcriptomes using cell population reference data".NATURE COMMUNICATIONS 8.-(2017):1856. |
入库方式： OAI收割
来源：上海营养与健康研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。