SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics

doi:10.1038/s41592-025-02968-w

2025-12-18

PRE

DOI：10.1038/s41592-025-02968-w

原文链接

原文求助

摘要

En 中文

基于成像的空间转录组学方法允许测量细胞表型的空间决定因素，但与基于随机条形码的克隆追踪方法不兼容，这阻碍了克隆驱动因素和空间驱动因素的同时检测。在此，我们报告了SpaceBar，它能够通过标准的基于成像的空间转录组学流程，同时实现克隆追踪和空间基因表达谱分析。我们的方法使用一个包含96种合成条形码序列的文库，对每个细胞进行组合标记。因此，SpaceBar能够在复杂组织背景下区分克隆动力学和环境驱动的转录调控。SpaceBar是一种细胞条形码策略，用于同时分析细胞的克隆身份和空间身份。

Keyword:

SpaceBar

clone tracing

spatial transcriptomics

cellular barcoding

gene expression profiling

期刊

Nature Methods

IF:

32.1

论文数:

7.2K

被引数:

12.7W

机构

Wistar Institute

学者数:

1.9K

论文数: 1.4K

被引数: 3.4K

university of pennsylvania

学者数:

9.2W

论文数: 7.8W

被引数: 153

引用论文

Vascular endothelial growth factor expression, angiogenesis, and necrosis in renal cell carcinomas 肾细胞癌中血管内皮生长因子的表达，血管生成和坏死

VIRCHOWS ARCHIV

IF3.1

2014-05-01

PREAI

Hemmerlein, B; Kugler, A; Özisik, R; Ringert, RH; Radzun, HJ; Thelen, P

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH MERFISH对小鼠初级运动皮层的空间分辨细胞图谱

Nature

IF0

2021-10-06

OAAI

Meng Zhang; Stephen W. Eichhorn; Brian Zingg; Zizhen Yao; Kaelan Cotter; Hongkui Zeng; Hongwei Dong; Xiaowei Zhuang

Synthetic recording and in situ readout of lineage information in single cells 单细胞谱系信息的合成记录和原位读出

Nature

IF0

2016-11-21

OAAI

Kirsten L. Frieda; James M. Linton; Sahand Hormoz; Joonhyuk Choi; Ke-Huan K. Chow; Zakary S. Singer; Mark W. Budde; Michael B. Elowitz; Long Cai

Biology and therapeutic targeting of vascular endothelial growth factor A 血管内皮生长因子A的生物学和治疗靶点

NATURE REVIEWS MOLECULAR CELL BIOLOGY

IF90.2

2023-07-25

109

PREAI

Perez-Gutierrez, Lorena; Ferrara, Napoleone

Massive multiplexing of spatially resolved single neuron projections with axonal BARseq 具有轴突BARseq的空间分辨单神经元投影的大规模复用

NATURE COMMUNICATIONS

IF15.7

2024-09-27

OAAI

Yuan, Li; Chen, Xiaoyin; Zhan, Huiqing; Henry, Gilbert L.; Zador, Anthony M.

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus 单细胞的原位转录谱分析揭示了小鼠海马中细胞的空间组织

NEURON

IF15

2016-10-01

547

OAAI

Shah, Sheel; Lubeck, Eric; Zhou, Wen; Cai, Long

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+通过RNA seqFISH在组织中进行转录组规模的超分辨成像

Nature

IF0

2019-03-25

OAAI

Chee-Huat Linus Eng; Michael Lawson; Qian Zhu; Ruben Dries; Noushin Koulena; Yodai Takei; Jina Yun; Christopher Cronin; Christoph Karp; Guo-Cheng Yuan; Long Cai

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics 单细胞和空间转录组学揭示的小鼠大脑中的克隆关系

Nature Neuroscience

IF0

2022-02-24

OAAI

Michael Ratz; Leonie von Berlin; Ludvig Larsson; Marcel Martin; Jakub Orzechowski Westholm; Gioele La Manno; Joakim Lundeberg; Jonas Frisén

Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells 药物治疗同质癌细胞后出现了不同的克隆命运

Nature

IF0

2023-07-19

OAAI

Yogesh Goyal; Gianna T. Busch; Maalavika Pillai; Jingxin Li; Ryan H. Boe; Emanuelle I. Grody; Manoj Chelvanambi; Ian P. Dardani; Benjamin Emert; Nicholas Bodkin; Jonas Braun; Dylan Fingerman; Amanpreet Kaur; Naveen Jain; Pavithran T. Ravindran; Ian A. Mellis; Karun Kiani; Gretchen M. Alicea; Mitchell E. Fane; Syeda Subia Ahmed; Haiyin Li; Yeqing Chen; Cedric Chai; Jessica Kaster; Russell G. Witt; Rossana Lazcano; Davis R. Ingram; Sarah B. Johnson; Khalida Wani; Margaret C. Dunagin; Alexander J. Lazar; Ashani T. Weeraratna; Jennifer A. Wargo; Meenhard Herlyn; Arjun Raj

Spatially resolved, highly multiplexed RNA profiling in single cells 单细胞中空间分辨的、高度多重的RNA分析

Science

IF0

2015-04-24

OAAI

Kok Hao Chen; Alistair N. Boettiger; Jeffrey R. Moffitt; Siyuan Wang; Xiaowei Zhuang

查看更多内容