Article
Immunology
Ryan Zander, Moujtaba Y. Kasmani, Yao Chen, Paytsar Topchyan, Jian Shen, Shikan Zheng, Robert Burns, Jennifer Ingram, Can Cui, Nikhil Joshi, Joseph Craft, Allan Zajac, Weiguo Cui
Summary: This study found that CD4(+) T cells consist of three distinct subsets during chronic viral infection, and IL-21 derived from Tfh cells is critical for sustaining CD8(+) T cell responses and viral control.
Article
Biotechnology & Applied Microbiology
Xinran Yang, Xinhao Ma, Chugang Mei, Linsen Zan
Summary: This study provides insights into the differential expression patterns of different types of RNA in intramuscular preadipocyte differentiation. It identifies key genes and networks related to intramuscular adipogenesis, providing data support for studying the molecular mechanisms of IMF deposition and potential markers for beef cattle breeding.
Article
Multidisciplinary Sciences
Alina Isakova, Norma Neff, Stephen R. Quake
Summary: Smart-seq-total is a method capable of assaying a broad spectrum of coding and noncoding RNA from a single cell, outperforming current RNA-seq protocols by capturing a wide range of transcripts. By analyzing the total RNAome of single cells, it can reveal new roles of noncoding RNA in essential processes such as cell cycle and embryonic development, as well as determine cell-type identity using different classes of short-noncoding RNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Jialu Hu, Mengjie Chen, Xiang Zhou
Summary: VIPCCA is a computational framework based on non-linear canonical correlation analysis for effective and scalable single cell data alignment. It combines deep learning for effective single cell data modeling and variational inference for scalable computation, enabling accurate alignment tasks across multiple samples and data types. VIPCCA is suitable for large-scale single cell analysis and can accommodate millions of cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Immunology
Junhong Wang, Xiaoxu Li, Yiyuan Lu, Quntao Huang, Yu Sun, Mingyang Cheng, Fengdi Li, Chunwei Shi, Yan Zeng, Chunfeng Wang, Xin Cao
Summary: This study utilized RNA-seq to analyze the expression profiles of lncRNAs and mRNAs in Zbtb1-deficient EL4 cells, revealing potential regulatory mechanisms of the Zbtb1 gene on various non-coding RNAs and coding RNAs.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Xu Yang, Jingzhang Ji, Hongdi Cui, Qi Zhao, Chunming Ding, Chang Xu
Summary: Long noncoding RNAs (lncRNAs) are found to play important roles in early embryonic development in pigs, including endogenous retrovirus-associated lncRNAs (ERV-lncRNAs). Two ERV-lncRNAs (TCONS_00035465 and TCONS_00031520) are identified as potential regulators in pig early embryo development.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Shuxia Li, Zhihao Cheng, Shiman Dong, Zhibo Li, Liangping Zou, Pingjuan Zhao, Xin Guo, Yan Bao, Wenquan Wang, Ming Peng
Summary: This study identified a novel cold-responsive intergenic lncRNA 1 (CRIR1) in cassava, which acts as a positive regulator of cold stress response by enhancing cold tolerance and modulating the translation efficiency of messenger RNA through interaction with cassava cold shock protein 5 (MeCSP5).
PLANT CELL AND ENVIRONMENT
(2022)
Article
Biotechnology & Applied Microbiology
Siew-Woh Choo, Yu Zhong, Edward Sendler, Anton -Scott Goustin, Juan Cai, Donghong Ju, Mary Ann Kosir, Roberta Giordo, Leonard Lipovich
Summary: This study investigates the impact of estrogen on transcription and translation in breast cancer cells. Through integrated analysis of RNA-Seq and Ribo-seq, it reveals distinct gene-specific responses to estrogen at the transcriptional and translational levels. The findings also indicate that most lncRNAs are not associated with ribosomes and are not affected by estrogen, while pseudogenes exhibit transcriptional and translational responses to estrogen.
Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Dakota Y. Hawkins, Daniel T. Zuch, James Huth, Nahomie Rodriguez-Sastre, Kelley R. McCutcheon, Abigail Glick, Alexandra T. Lion, Christopher F. Thomas, Abigail E. Descoteaux, William Evan Johnson, Cynthia A. Bradham
Summary: In this study, a novel unsupervised algorithm called ICAT is proposed, which can accurately identify and resolve cell states in single-cell RNA sequencing experiments, especially in perturbation experiments, where cell states need to be matched and population substructure needs to be removed. Through validation using simulated and real datasets, it is shown that ICAT outperforms current integration workflows and is robust to various conditions. Empirical validation in a developmental model demonstrates that only ICAT can identify perturbation-unique cellular responses.
Article
Biochemical Research Methods
Ling-Ling Zheng, Jing-Hua Xiong, Wu-Jian Zheng, Jun-Hao Wang, Zi-Liang Huang, Zhi-Rong Chen, Xin-Yao Sun, Yi-Min Zheng, Ke-Ren Zhou, Bin Li, Shun Liu, Liang-Hu Qu, Jian-Hua Yang
Summary: The study developed ColorCells, a resource for comparative analysis of lncRNAs expression, classification, and functions in single-cell RNA-Seq data, identifying many cell-specific lncRNAs that show expression variability between different cell clusters and possess comparable cell classification ability to known marker genes; the cell-specific lncRNAs have been validated through in vitro experiments, and it was found that lncRNAs are typically co-expressed with mRNAs in the same cell cluster, which can help uncover their functions.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Immunology
Ming Yang, Pengpeng Cao, Zhidan Zhao, Zheyu Wang, Chen Jia, Yunkai Guo, Heng Yin, Ming Zhao, Yan Ding, Haijing Wu, Qianjin Lu
Summary: In this study, we investigated the expression levels of CCR4, CCR6 and CXCR3 on Tfh-like cells in the peripheral blood and skin lesions of SLE patients and normal controls. The results showed a decreased expression of CXCR3 on Tfh-like cells in lupus peripheral blood, while an increased expression was observed in skin lesions. Additionally, higher levels of CXCR3 were found in Tfh cells from human tonsils, suggesting a potential role of CXCR3 in guiding Tfh-like cells to migrate to inflammatory sites.
CLINICAL IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Biochemical Research Methods
Qianqian Zhang, Xing Xu, Li Lin, Jian Yang, Xing Na, Xin Chen, Lingling Wu, Jia Song, Chaoyong Yang
Summary: Cilo-seq is a high-performance platform for single-cell RNA sequencing library construction. It utilizes digital microfluidics in a single device, enabling convenient single-cell isolation, efficient nucleic acid amplification, low-loss nucleic acid purification, and high-quality library preparation.