Think twice: how single-cell suspensions from solid tissues for single-cell transcriptomics are well prepared by Meng-Meng Qu, Yan-Mei Jiao, Haijuan Wang

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Single-cell and spatial transcriptomics in endocrine research by Ryusaku Matsumoto, Takuya Yamamoto

“…Additionally, we also summarize the potential future applications of single-cell and spatial transcriptomics in the study of endocrine organs and their disorders.…”
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Identification of malignant cells in single-cell transcriptomics data by Massimo Andreatta, Josep Garnica, Santiago Javier Carmona

“…Abstract Single-cell transcriptomics has significantly advanced our ability to uncover the cellular heterogeneity of tumors. …”
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Transcriptomics, single-cell sequencing and spatial sequencing-based studies of cerebral ischemia by Jiaming Liu, Tao Qing, Mei he, Liu Xu, Zhuxiang Wu, Meiting Huang, Zheyu Liu, Ye Zhang, Zisheng Li, Wenhui Yang, Junbo Liu, Jie Li

“…To comprehensively understand the pathophysiological process of cerebral ischemia and to find new therapeutic strategies, a new approach to cerebral ischemia transcriptomics has emerged in recent years. By integrating data from multiple levels of transcriptomics, such as transcriptomics, single-cell transcriptomics, and spatial transcriptomics, this new approach can provide powerful help in revealing the molecular mechanisms of cerebral ischemia occurrence and development. …”
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Advances in Microfluidic Single-Cell RNA Sequencing and Spatial Transcriptomics by Yueqiu Sun, Nianzuo Yu, Junhu Zhang, Bai Yang

“…Here, we survey the current landscape of microfluidic methods in the field of single-cell and spatial multi-omics, as well as assessing their relative advantages and limitations. …”
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Three-dimensional single-cell transcriptome imaging of thick tissues by Rongxin Fang, Aaron Halpern, Mohammed Mostafizur Rahman, Zhengkai Huang, Zhiyun Lei, Sebastian J Hell, Catherine Dulac, Xiaowei Zhuang

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Single-cell transcriptomic analysis of chondrocytes in cartilage and pathogenesis of osteoarthritis by Changyuan Huang, Bin Zeng, Bo Zhou, Guanming Chen, Qi Zhang, Wenhong Hou, Guozhi Xiao, Li Duan, Ni Hong, Wenfei Jin

“…Here, we constructed a single-cell transcriptomic atlas of chondrocytes in healthy cartilage and identified nine chondrocyte subsets including homeostatic chondrocytes, proliferate fibrochondrocytes, and hypertrophic chondrocytes (HTC). …”
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Reconstruction of gene regulatory networks from single cell transcriptomic data by M. A. Rybakov, N. A. Omelyanchuk, E. V. Zemlyanskaya

“…This review describes the approaches and programs that are used to reconstruct GRNs from single-cell RNA sequencing (scRNA-seq) data. We consider the advantages of using scRNA-seq data compared to bulk RNA-seq, as well as challenges in GRN inference. …”
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Single-cell transcriptomic atlas of enteroendocrine cells along the murine gastrointestinal tract. by Christopher A Smith, Elisabeth A A O'Flaherty, Nunzio Guccio, Austin Punnoose, Tamana Darwish, Jo E Lewis, Rachel E Foreman, Joyce Li, Richard G Kay, Alice E Adriaenssens, Frank Reimann, Fiona M Gribble

“…The objective of this study was to generate a comprehensive transcriptomic map of mouse EECs from the stomach to the rectum.…”
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Comprehensive analysis of Metacrinus rotundus full length transcriptome by Zhong Li, Yue Dong, Xuebao He, Chen Han, Xiaomei Liao, Jing Mo, Qian Zhang, Xuelei Zhang, Zongling Wang, Qinzeng Xu

“…Our study enhances understanding of the characteristics of M. rotundus transcriptome and provides a valuable genetic resource for further studies on adaptive evolution in this species, as well as in other crinoids.…”
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Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics. by Kenneth D Harris, Hannah Hochgerner, Nathan G Skene, Lorenza Magno, Linda Katona, Carolina Bengtsson Gonzales, Peter Somogyi, Nicoletta Kessaris, Sten Linnarsson, Jens Hjerling-Leffler

“…These results elucidate the complexity of inhibitory neurons in one of the simplest cortical structures and show that characterizing these cells requires continuous modes of variation as well as discrete cell classes.…”
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An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics by Shaobo Wang, Qiong Zhang, Hui Hui, Kriti Agrawal, Maile Ann Young Karris, Tariq M. Rana

“…Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). …”
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Based on single-cell and transcriptome data, ferroptosis and the immunological landscape in osteosarcoma were discovered by Yingcun Jiang, Chao Song, Jiyuan Yan, Liang Luo, Silong Gao, Feng Jiang, Zhangchao Wei, Jinwen Chen, Zongchao Liu, Jianhua Ge

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Single-cell technologies and spatial transcriptomics: decoding immune low - response states in endometrial cancer by Yumeng Li, Hua Qiu, Zhenzhen Zhao, Fanghua Qi, Pingping Cai

“…To tackle this challenge, single-cell sequencing and spatial transcriptomics (ST) are increasingly applied. …”
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Transcriptomics, lipidomics, and single-nucleus RNA sequencing integration: exploring sphingolipids in MASH-HCC progression by Jing Zeng, Grayson Way, Nan Wu, Xixian Jiang, Yun-ling Tai, Derrick Zhao, Lianyong Su, Qianhua Yan, Xuan Wang, Emily C. Gurley, Phillip B. Hylemon, Sayed Obaidullah Aseem, Arun J. Sanyal, Jiangao Fan, Huiping Zhou

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Single-cell transcriptome reveals the reprogramming of immune microenvironment during the transition from MASH to HCC by Yu Huang, Ying Xie, Yuqing Zhang, Zhemian Liu, Weihua Jiang, Yingying Ye, Jiale Tang, Zhenhua Li, Zhinan Yin, Xue-Jia Lin

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Single-cell transcriptomic analysis reveals metastatic and immunosuppressive characteristics in meningioma brain-tumor interface by Boya Huang, Jinlian Liang, Xiaogen Tang, Yue Zhu, Lijuan Gao, Dongwei Fu, Cheng Wei, Yifang Li, Chao Ke, Hongyi Zhang, Oscar Junhong Luo

“…Methods To identify biomarkers of early metastasis and discover potential therapeutic targets, we integrated single-cell transcriptome datasets of meningioma, and identified the cell populations and molecular signatures uniquely present at the BTI. …”
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Single cell transcriptome sequencing indicates the cellular heterogeneity of small intestine tissue in celiac disease by Tian Shi, Yan Feng, Jin Ma, Weidong Liu, Na Li, Ting Li, Adilai Abudurexiti, Ailifeire Tuerxuntayi, Shenglong Xue, Feng Gao

“…We aimed to construct a single cell transcriptome spectrum, analyze the immune microenvironment and cellular heterogeneity, discover disease-related specific genes and markers, and explore the pathogenesis of CeD. …”
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Integrated single-cell chromatin and transcriptomic analyses of peripheral immune cells in patients with alopecia areata by Jesus Gay-Mimbrera, Pedro Jesús Gómez-Arias, Pedro Jesús Gómez-Arias, Pablo Álvarez-Heredia, Alexander Batista-Duharte, Irene Rivera-Ruiz, Macarena Aguilar-Luque, Miguel Juan-Cencerrado, Miguel Juan-Cencerrado, Carmen Mochón-Jiménez, Carmen Mochón-Jiménez, Álvaro Cebrián-García, Eloísa Andújar-Pulido, Mónica Pérez-Alegre, Alejandra Pera, Alejandra Pera, Juan Ruano, Juan Ruano, Juan Ruano

“…While prior research has primarily focused on lesional skin, the contribution of systemic immune cells remains underexplored.MethodsWe performed integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on peripheral blood mononuclear cells (PBMCs) from patients with mild and severe AA, as well as healthy controls. …”
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Single-Cell and Single-Nuclei transcriptomics profiling reveals dynamic cellular features in tumor-related adipose microenvironment of breast cancer patients with high BMI by Xiaoxiao Hu, Fang Jia, Lili Li, Wuzhen Chen, Leyi Zhang, Jun Pan, Sangsang Zhu, Zhen Wang, Jian Huang

“…Materials and methods: We unveiled a comprehensive cell atlas by employing single-cell (N = 27) and single-nuclei (N = 6) transcriptomics to address dynamic changes of immune and stromal cell components within WAT in high BMI population. …”
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