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Fundamental and practical approaches for single-cell ATAC-seq analysis

aBIOTECH 2022年第3期3卷 212-223页

作者： Peiyu Shi Yage Nie Jiawen Yang Weixing Zhang Zhongjie Tang Jin Xu State Key Laboratory of Biocontrol School of Life SciencesSun Yat-Sen UniversityGuangzhou510275China Zhongshan School of Medicine Sun Yat-Sen UniversityGuangzhou510275China

Assays for transposase-accessible chromatin through high-throughput sequencing(ATAC-seq)are effective tools in the study of genome-wide chromatin accessibility *** the rapid development of single-cell technology,open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq *** application of scATAC-seq has become as popular as that of ***,owing to the nature of scATAC-seq data,which are sparse and noisy,processing the data requires different methodologies and empirical *** review presents a practical guide for processing scATAC-seq data,from quality evaluation to downstream analysis,for various *** addition to the epigenomic profiling from scATAC-seq,we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell *** anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.

关键词： Chromatin accessibility scATAC-seq Data analysis bioinformatic tools

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Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

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Journal of Genetics and Genomics 2023年第9期50卷 625-640页

作者： Mengnan Cheng Yujia Jiang Jiangshan Xu Alexios-Fotios AMentis Shuai Wang Huiwen Zheng Sunil Kumar Sahu Longqi Liu Xun Xu BGI-Hangzhou HangzhouZhejiang 310012China BGI-Shenzhen ShenzhenGuangdong 518103China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China Guangdong Provincial Key Laboratory of Genome Read and Write ShenzhenGuangdong 518120China

The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the scientific community has been able to visualize life at an unprecedented *** recently,the Spatially Resolved Transcriptomics(SRT)technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life,including the origin of different cellular populations developed from totipotent cells and human *** this review,we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools,as well as the representative SRT *** the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects,we can foresee the bright future of such new tools in understanding life at the most profound analytical level.

关键词： Spatially resolved transcriptomics bioinformatic tools Spatial single-cell Cell communications Tissue dissection Three-dimensional organ

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bioinformatic approaches of liquid-liquid phase separation in human disease

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Chinese Medical Journal 2024年第16期137卷 1912-1925页

作者： Jun Sun Yilong Chen Ruiye Bi Yong Yuan Haopeng Yu Department of Thoracic Surgery and West China Biomedical Big Data Center West China HospitalSichuan UniversityChengduSichuan 610041China Med-X Center for Informatics Sichuan UniversityChengduSichuan 610041China Department of Orthognathic and TMJ Surgery State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduSichuan 610041China

Biomolecular aggregation within cellular environments via liquid-liquid phase separation(LLPS)spontaneously forms droplet-like structures,which play pivotal roles in diverse biological *** structures are closely associated with a range of diseases,including neurodegenerative disorders,cancer and infectious diseases,highlighting the significance of understanding LLPS mechanisms for elucidating disease pathogenesis,and exploring potential therapeutic *** this review,we delineate recent advancements in LLPS research,emphasizing its pathological relevance,therapeutic considerations,and the pivotal role of bioinformatic tools and databases in facilitating LLPS ***,we undertook a comprehensive analysis of bioinformatic resources dedicated to LLPS research in order to elucidate their functionality and *** providing comprehensive insights into current LLPS-related bioinformatics resources,this review highlights its implications for human health and disease.

关键词： Phase separation Liquid-liquid phase separation Disease Phase separation databases bioinformatic tools

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