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
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
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.
Article
Genetics & Heredity
Juber Herrera-Uribe, Jayne E. Wiarda, Sathesh K. Sivasankaran, Lance Daharsh, Haibo Liu, Kristen A. Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal L. Loving, Christopher K. Tuggle
Summary: The study conducted transcriptome analysis of pig peripheral blood immune cells at both bulk and single-cell levels, identifying different cell types and their associated gene expression features. The research demonstrated significant correlations in gene expression between pig cells and human PBMC data, providing insights into the similarities between pig and human immune systems.
FRONTIERS IN GENETICS
(2021)
Article
Immunology
Emil Lagumdzic, Clara P. S. Pernold, Reinhard Ertl, Nicola Palmieri, Maria Stadler, Spencer Sawyer, Melissa R. Stas, Heinrich Kreutzmann, Till Ruemenapf, Andrea Ladinig, Armin Saalmueller
Summary: The expression profiles of PBMCs and CD8(+) T cells were investigated after PRRSV AUT15-33 infection. PBMCs showed a strong innate immune response at 7 dpi, and CD8(+) T cells exhibited a strong adaptive immune response starting from 14 dpi. The gene expression patterns of both cell types provided valuable insights into the immune response to PRRSV infection and could serve as potential biomarkers for vaccine and therapeutics development.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jingyue Xi, Sung Rye Park, Jun Hee Lee, Hyun Min Kang
Summary: SiftCell is a suite of software tools that can identify and visualize cell-containing and cell-free droplets, as well as quantify the contribution of ambient RNAs for each droplet. It provides a more comprehensive and accurate way to perform upstream quality control in scRNA-seq than existing methods.
Article
Biochemical Research Methods
Johannes Bues, Marjan Biocanin, Joern Pezoldt, Riccardo Dainese, Antonius Chrisnandy, Saba Rezakhani, Wouter Saelens, Vincent Gardeux, Revant Gupta, Rita Sarkis, Julie Russeil, Yvan Saeys, Esther Amstad, Manfred Claassen, Matthias P. Lutolf, Bart Deplancke
Summary: DisCo is a deterministic droplet microfluidics tool that enables high-resolution snapshots of cellular heterogeneity in small, individual tissues, revealing important cell types and subtypes.
Article
Biochemistry & Molecular Biology
Jacob C. Kimmel, David R. Kelley
Summary: scNym is a semi-supervised adversarial neural network that can transfer cell identity annotations between different experiments by learning rich representations of cell identities from both labeled and unlabeled datasets. It shows superior performance in transferring annotations across experiments and can synthesize information from multiple datasets to improve accuracy. Additionally, scNym models are well calibrated, interpretable, and can be enhanced with saliency methods.
Article
Biochemistry & Molecular Biology
Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen
Summary: DISCO is an integrated database of single-cell omics data, offering an integrated cell atlas and harmonized metadata that users can utilize for comprehensive single-cell data analysis and exploration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Qing Tian, Jia-Peng He, Can Zhu, Qiu-Yang Zhu, Yu-Gu Li, Ji-Long Liu
Summary: This study used single-cell RNA sequencing to investigate the molecular mechanism of embryo implantation in pigs. The researchers analyzed the interaction between embryo cells and maternal endometrial cells and identified global gene expression changes associated with embryo implantation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xin Shao, Haihong Yang, Xiang Zhuang, Jie Liao, Penghui Yang, Junyun Cheng, Xiaoyan Lu, Huajun Chen, Xiaohui Fan
Summary: scDeepSort is a pre-trained tool for cell-type annotation in single-cell transcriptomics using deep learning and a weighted graph neural network. It demonstrates high performance and robustness across multiple datasets, achieving an accuracy of 83.79%.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Daniel Crespo-Piazuelo, Herve Acloque, Olga Gonzalez-Rodriguez, Mayrone Mongellaz, Marie-Jose Mercat, Marco C. A. M. Bink, Abe E. Huisman, Yuliaxis Ramayo-Caldas, Juan Pablo Sanchez, Maria Ballester
Summary: Genome-wide association studies on pigs have identified millions of significant associations between genetic polymorphisms and the expression of genes in the duodenum, liver, and muscle. These findings shed light on the regulatory variations that shape end-trait phenotypes and provide valuable insights into molecular mechanisms.
Article
Agriculture, Dairy & Animal Science
Kyu-Sang Lim, Sun-Sik Chang, Bong-Hwan Choi, Seung-Hwan Lee, Kyung-Tai Lee, Han-Ha Chai, Jong-Eun Park, Woncheoul Park, Dajeong Lim
Article
Biotechnology & Applied Microbiology
Yulu Chen, Laura E. Tibbs Cortes, Carolyn Ashley, Austin M. Putz, Kyu-Sang Lim, Michael K. Dyck, Frederic Fortin, Graham S. Plastow, Jack C. M. Dekkers, John C. S. Harding, Pig Gen Canada
Article
Biotechnology & Applied Microbiology
Kyu-Sang Lim, Jian Cheng, Austin Putz, Qian Dong, Xuechun Bai, Hamid Beiki, Christopher K. Tuggle, Michael K. Dyck, Pig Gen Canada, Frederic Fortin, John C. S. Harding, Graham S. Plastow, Jack C. M. Dekkers
Summary: Investigation of gene expression profiles in blood of young healthy pigs revealed associations with disease resilience, growth rate, health scores, mortality, and feed conversion rate. Genes involved in stress response, heme metabolism, and viral gene expression were found to be associated with host response to disease.
Article
Agriculture, Dairy & Animal Science
Qian Dong, Jenelle Dunkelberger, Kyu-Sang Lim, Joan K. Lunney, Christopher K. Tuggle, Raymond R. R. Rowland, Jack C. M. Dekkers
Summary: Natural genetic variants in the CD163, CD169, and RGS16 genes are associated with resistance to PRRSV and/or PCV2b infection and appear to interact with the resistance quantitative trait locus in the GBP5 gene. The identified SNPs can be used to select for increased natural resistance to PRRSV and/or PRRSV-PCV2b coinfection.
JOURNAL OF ANIMAL SCIENCE
(2021)
Review
Cell Biology
Joan K. Lunney, Angelica Van Goor, Kristen E. Walker, Taylor Hailstock, Jasmine Franklin, Chaohui Dai
Summary: Pigs have significant potential as biomedical models for studying human developmental processes, congenital diseases, and pathogen response mechanisms, as well as serving as xenotransplant organ donors and tools for vaccine and drug design. The similarities between pigs and humans in anatomy, physiology, immunology, and genetics enhance their potential as human models. Therefore, utilizing animal models that closely resemble humans, such as pigs, is crucial for relevant and reproducible research.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Immunology
Jean N. Manirarora, Kristen E. Walker, Veerupaxagouda Patil, Gourapura J. Renukaradhya, Joanna LaBresh, Yvonne Sullivan, Ore Francis, Joan K. Lunney
Summary: This study aimed to generate priority immune reagents for pigs and market them. Soluble swine cytokines and monoclonal antibodies (mAbs) were successfully produced. These new antibodies have expanded opportunities for immunology research in swine.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Kyu-Sang Lim, Hyung-Chul Kim, Bong-Hwan Choi, Ju-Whan Son, Kyung-Tai Lee, Tae-Jeong Choi, Yong-Min Cho, Han-Ha Chai, Jong-Eun Park, Woncheoul Park, Chiwoong Lim, Jun-Mo Kim, Dajeong Lim
Summary: In this study, genes with monoallelic expression were identified in Korean cattle (Hanwoo) using genome-wide and transcriptome-wide screening. Tissue-specific expression patterns were observed, and these genes were associated with breeding values for economically important traits in Hanwoo. This study provides potential selective targets for genetic improvement in Hanwoo.
Article
Agriculture, Dairy & Animal Science
Young-Jun Seo, Byeonghwi Lim, Do-Young Kim, Kyu-Sang Lim, Jun-Mo Kim
Summary: This study utilized RNA-sequencing analysis to investigate transcriptomic changes in backfat tissue of Korean native pigs and Yorkshire pig crossbreeds during growth and finishing stages. Differential gene expression was found to be significantly influenced by lipid metabolism and hormonal changes. Differentially expressed genes were associated with lipid metabolism, growth, and maturation-related terminologies, with LEP and ACTC1 identified as core genes in the functional gene network analysis. The study provides a comprehensive understanding of the contribution of backfat tissue to crossbreeds of Korean native pigs and Yorkshire pigs during growth periods.
Article
Agriculture, Dairy & Animal Science
Do-Young Kim, Byeonghwi Lim, Dajeong Lim, Woncheol Park, Kyung-Tai Lee, Eun-Seok Cho, Kyu-Sang Lim, Si Nae Cheon, Bong-Hwan Choi, Jong-Eun Park, Jun-Mo Kim
Summary: Fat is involved in the synthesis of fatty acids, circulation of fatty acids, and lipid metabolism. This study aimed to investigate the epigenetic differences in abdominal fat during the growth of pigs. The results showed changes in DNA methylation and gene expression with growth. Genes that were differentially methylated or expressed were found to be involved in immune response and lipid metabolism. The effects of DNA methylation on gene expression were analyzed through cis-regulation and trans-regulation analysis. This research provides insights into the underlying mechanisms of epigenetic regulation in porcine abdominal fat during aging.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Yulu Chen, Steven Lonergan, Kyu-Sang Lim, Jian Cheng, Austin M. Putz, Michael K. Dyck, PigGen Canada, Frederic Fortin, John C. S. Harding, Graham S. Plastow, Jack C. M. Dekkers
Summary: This study found that plasma protein levels can be used as an indicator to select pigs with disease resilience, as they are genetically correlated with disease resilience. Therefore, plasma protein levels have the potential to be used as a tool for pig breeding and management.
JOURNAL OF ANIMAL SCIENCE
(2023)
Correction
Agriculture, Dairy & Animal Science
Do-Young Kim, Byeonghwi Lim, Dajeong Lim, Woncheol Park, Kyung-Tai Lee, Eun-Seok Cho, Kyu-Sang Lim, Si Nae Cheon, Bong-Hwan Choi, Jong-Eun Park, Jun-Mo Kim
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Angelica Van Goor, Alex Pasternak, Kristen Walker, Linjun Hong, Carolina Malgarin, Daniel J. MacPhee, John C. S. Harding, Joan K. Lunney
Article
Veterinary Sciences
Byeonghwi Lim, Sangwook Kim, Kyu-Sang Lim, Chang-Gi Jeong, Seung-Chai Kim, Sang-Myeong Lee, Choi-Kyu Park, Marinus F. W. te Pas, Haesu Gho, Tae-Hun Kim, Kyung-Tai Lee, Won-Il Kim, Jun-Mo Kim
VETERINARY RESEARCH
(2020)