iPscDB: a comprehensive platform for plant single-cell transcriptomic data integration and analysis

Peng Lü

doi:10.1093/nar/gkag909

2026-09-18

DOI：10.1093/nar/gkag909

原文链接

查看原文

摘要

En 中文

单细胞技术的快速进步显著增强了我们探究植物组织内细胞异质性的能力。然而，解析这些复杂的细胞景观需要处理高维基因表达矩阵并整合多样本数据集，以实现准确的标记物选择、细胞识别及其他复杂计算操作。这些流程通常需要广泛的编程专业知识，对计算背景有限的科研人员构成挑战。为解决此问题，我们开发了整合型植物单细胞数据库（iPscDB），一个集成且多功能的平台，用于促进植物单细胞数据的整合与分析。iPscDB整合了来自38个植物物种946项实验的4 688 428个细胞和288 139个经过筛选的细胞标记物。在原始数据可用的情况下，数据集均通过统一的单一流程重新处理，并对整合质量和自动细胞类型注释进行了定量基准测试。该平台引入了标记物置信度等级方案，根据支持证据的强度和独立性（从人工筛选的经典标记物到数据库衍生的关联）对每个细胞类型标记物进行分级，使用户可直接判断标记物的可靠性。该平台还提供用户友好的在线分析流程和模块，可处理原始FASTQ文件或Cell Ranger处理过的文件。用户可通过直观界面配置参数，并利用集成图像编辑器定制可视化输出。此外，iPscDB支持多种分析，包括跨物种基因表达、电子单细胞图谱以及发育轨迹。通过简化单细胞转录组学的复杂工作流程，iPscDB为具有不同技术背景的研究人员提供了一个实用且易于访问的资源。iPscDB可访问网址：https://www.tobaccodb.org/ipscdb/homePage。

AI总结

对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。

期刊

Nucleic Acids Research

IF:

13.1

论文数:

3.6W

被引数:

29.0W

机构

Guizhou Academy of Tobacco Science

学者数:

论文数: 7

被引数: 0

zhejiang university

学者数:

8.7K

论文数: 2.5K

被引数: 0

beijing life science academy

学者数:

论文数: 21

被引数: 0

Henan University

学者数:

1.3K

论文数: 375

被引数: 0

查看更多机构

引用论文

Comprehensive analysis of multi-omics single-cell data using the single-cell analyst 使用Single-Cell Analyst对多组学单细胞数据进行综合分析

iMeta

IF33.2

2025-04-28

OAAI

Lu Pan; Bufu Tang; Xuan Zhang; Paolo Parini; Roman Tremmel; Joseph Loscalzo; Volker M. Lauschke; Bradley A. Maron; Paola Paci; Ingemar Ernberg; Nguan Soon Tan; Ákos Végvári; Zehuan Liao; Sundararaman Rengarajan; Roman Zubarev; Yuxuan Fan; Xu Zheng; Xinyue Jian; Ren Sheng; Zhenning Wang; Xuexin Li; Lu Pan; Bufu Tang; Xuan Zhang; Paolo Parini; Roman Tremmel; Joseph Loscalzo; Volker M. Lauschke; Bradley A. Maron; Paola Paci; Ingemar Ernberg

The Sequence Read Archive 序列读取存档

NUCLEIC ACIDS RESEARCH

IF13.1

2010-11-09

2.0K

OAAI

Leinonen, Rasko; Sugawara, Hideaki; Shumway, Martin

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data

Methods in Molecular Biology

IF0

2016-12-17

PREAI

Dan M. Bolser; Daniel M. Staines; Emily Perry; Paul J. Kersey

Plant Single Cell Transcriptome Hub (PsctH): an integrated online tool to explore the plant single-cell transcriptome landscape 植物单细胞转录组中心 (PsctH): 一个探索植物单细胞转录组景观的集成在线工具

PLANT BIOTECHNOLOGY JOURNAL

IF10.5

2021-10-26

OAAI

Xu, Zhongping; Wang, Qiongqiong; Zhu, Xiangqian; Wang, Guanying; Qin, Yuan; Ding, Fang; Tu, Lili; Daniell, Henry; Zhang, Xianlong; Jin, Shuangxia

Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings

NATURE PLANTS

IF13.6

2023-10-30

OAAI

Han, Xue; Zhang, Yilin; Lou, Zhiying; Li, Jian; Wang, Zheng; Gao, Chunlei; Liu, Yi; Ren, Zizheng; Liu, Weimin; Li, Bosheng; Pan, Wenbo; Zhang, Huawei; Sang, Qing; Wan, Miaomiao; He, Hang; Deng, Xing Wang

CellTracer: a comprehensive database to dissect the causative multilevel interplay contributing to cell development trajectories

NUCLEIC ACIDS RESEARCH

IF13.1

2022-10-16

OAAI

Guo, Qiuyan; Wang, Peng; Liu, Qian; Hao, Yangyang; Gao, Yue; Qi, Yue; Xu, Rongji; Chen, Hongyan; Xin, Mengyu; Wu, Xiaoting; Sun, Rui; Zhi, Hui; Zhang, Yunpeng; Ning, Shangwei; Li, Xia

The Human Cell Atlas 人类细胞图谱

eLife

IF0

2017-12-05

OAAI

Aviv Regev; Sarah A Teichmann; Eric S Lander; Ido Amit; Christophe Benoist; Ewan Birney; Bernd Bodenmiller; Peter Campbell; Piero Carninci; Menna Clatworthy; Hans Clevers; Bart Deplancke; Ian Dunham; James Eberwine; Roland Eils; Wolfgang Enard; Andrew Farmer; Lars Fugger; Berthold Göttgens; Nir Hacohen; Muzlifah Haniffa; Martin Hemberg; Seung Kim; Paul Klenerman; Arnold Kriegstein; Ed Lein; Sten Linnarsson; Emma Lundberg; Joakim Lundeberg; Partha Majumder; John C Marioni; Miriam Merad; Musa Mhlanga; Martijn Nawijn; Mihai Netea; Garry Nolan; Dana Pe'er; Anthony Phillipakis; Chris P Ponting; Stephen Quake; Wolf Reik; Orit Rozenblatt-Rosen; Joshua Sanes; Rahul Satija; Ton N Schumacher; Alex Shalek; Ehud Shapiro; Padmanee Sharma; Jay W Shin; Oliver Stegle; Michael Stratton; Michael J T Stubbington; Fabian J Theis; Matthias Uhlen; Alexander van Oudenaarden; Allon Wagner; Fiona Watt; Jonathan Weissman; Barbara Wold; Ramnik Xavier; Nir Yosef

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants 单细胞拟南芥根图谱揭示了野生型和细胞身份突变体的发育轨迹

DEVELOPMENTAL CELL

IF8.7

2022-02-01

130

OAAI

Shahan, Rachel; Hsu, Che-Wei; Nolan, Trevor M.; Cole, Benjamin J.; Taylor, Isaiah W.; Greenstreet, Laura; Zhang, Stephen; Afanassiev, Anton; Vlot, Anna Hendrika Cornelia; Schiebinger, Geoffrey; Benfey, Philip N.; Ohler, Uwe

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors DoubletFinder: 使用人工最近邻在单细胞RNA测序数据中进行双峰检测

CELL SYSTEMS

IF7.7

2019-04-01

1.7K

OAAI

McGinnis, Christopher S.; Murrow, Lyndsay M.; Gartner, Zev J.

Construction of a cross-species cell landscape at single-cell level 在单细胞水平上构建跨物种细胞景观

NUCLEIC ACIDS RESEARCH

IF13.1

2022-08-05

OAAI

Wang, Renying; Zhang, Peijing; Wang, Jingjing; Ma, Lifeng; Weigao, E.; Suo, Shengbao; Jiang, Mengmeng; Li, Jiaqi; Chen, Haide; Sun, Huiyu; Fei, Lijiang; Zhou, Ziming; Zhou, Yincong; Chen, Yao; Zhang, Weiqi; Wang, Xinru; Mei, Yuqing; Sun, Zhongyi; Yu, Chengxuan; Shao, Jikai; Fu, Yuting; Xiao, Yanyu; Ye, Fang; Fang, Xing; Wu, Hanyu; Guo, Qile; Fang, Xiunan; Li, Xia; Gao, Xianzhi; Wang, Dan; Xu, Peng-Fei; Zeng, Rui; Xu, Gang; Zhu, Lijun; Wang, Lie; Qu, Jing; Zhang, Dan; Ouyang, Hongwei; Huang, He; Chen, Ming; Ng, Shyh-Chang; Liu, Guang-Hui; Yuan, Guo-Cheng; Guo, Guoji; Han, Xiaoping

查看更多内容