Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq by Hefei Zhang, Xuhang Li, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Kucukural, Jingyi Jessica Li, Manuel Garber, Albertha J. M. Walhout

“…Abstract Transcriptomes provide highly informative molecular phenotypes that, combined with gene perturbation, can connect genotype to phenotype. …”
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Prognosis Signature of Cuprotosis-Related lncRNAs Associated with Kidney Renal Clear Cell Carcinoma by Yiren Gao, Zhen Jia

“…The Cancer Genome Atlas (TCGA) database was analyzed, and the transcriptome data and clinical information on the patients with KIRC were obtained. …”
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Integrated analysis of miRNAs-mRNAs in skeletal muscle development revealed that novel-miR-766 affects myoblast differentiation and myofiber-type formation in sheep by Zhenzhen Gu, Zhenzhen Gu, WeiWei Duan, WeiWei Duan, Chenxi Liu, Chenxi Liu, Chenxi Liu, Wenrong Li, Wenrong Li, Wenrong Li, Bin Han, Bin Han, Bin Han, Mingjun Liu, Mingjun Liu, Mingjun Liu, Mingjun Liu

“…Method: To identify key miRNAs and target genes associated with muscle development, embryos or longissimus dorsi of Chinese Merino sheep were collected for whole-transcriptome sequencing across 11 gestation periods: 26 days (D26), D29, D32, D35, D40, D45, D55, D75, D85, D105, and D135. …”
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Construction and Evaluation of a Rat Model of Abnormal Uterine Bleeding by LIAN Hui, JIANG Yanling, LIU Jia, ZHANG Yuli, XIE Wei, XUE Xiaoou, LI Jian

“…After comparing the transcriptome sequencing results of uterine tissues between AUB and normal rats, a total of 4 723 differentially expressed genes were identified, including 2 191 up-regulated genes and 2 532 down-regulated genes. …”
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Regulation and functions of alternative polyadenylation in fungi by Lei Zhang, Xiaoling Deng, Wenshuai Ma, Tianjiao Zhou, Chuan Xu

“…Understanding the comprehensive landscape of APA can provide valuable insights into the complexity of gene regulation. …”
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Inhibiting ANP32E protects against acute kidney injury by regulating autophagy via the AMPK pathway by Chunjie Wang, Fang Bai, Luyao Li, Kuipeng Yu, Xiangdong Yang

“…In summary, these findings suggest that ANP32E plays a role in pathogenesis and provide a new avenue for the treatment of acute ischemic kidney injury.…”
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Selenium-Biofortified Alfalfa Hay Supplemented to Jersey and Holstein Dairy Heifers During the Peripartum Period: Effects on Dams and Their Offspring by Shana Jaaf, Matteo Mezzetti, Sebastiano Busato, Erminio Trevisi, Massimo Bionaz

“…Overall, our data did not support the hypothesis that supplementing Se-biofortified hay to pregnant heifers improves their performance and the health of dams and offspring, at least at the dose we provided.…”
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Cut&tag: a powerful epigenetic tool for chromatin profiling by Zhijun Fu, Sanjie Jiang, Yiwen Sun, Shanqiao Zheng, Liang Zong, Peipei Li

“…Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. …”
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Immune System Perspective in Intracerebral Hemorrhage Research: A Focus on Monocytes and Macrophages by Hang Hang, Lei Huang, Yuanhong Mao, Guofeng Wu

“…These research advancements aim to provide new insights for improving the diagnosis and treatment strategies for ICH.…”
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Single-Cell Sequencing Analysis Based on Public Databases for Constructing a Metastasis-Related Prognostic Model for Gastric Cancer by Rubin Xu, Liang Chen, Wei Wei, Qikai Tang, You Yu, Yiming Hu, Sultan Kadasah, Jiaheng Xie, Hongzhu Yu

“…Conclusions. Our study could provide new ideas for the treatment of gastric cancer.…”
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Evolution and comparison of the expression of TCP genes in the benincaseae and cucurbiteae tribes by Shuoshuo Wang, Wenli Li, Han Jin

“…In conclusion, this is the first systematic analysis of TCP genes in Cucurbitaceae, which provides deeper insights into their evolutionary dynamics and functional properties, which may be crucial for the genetic improvement of Cucurbitaceae.…”
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Transcellular chaperone signaling is an intercellular stress-response distinct from the HSF-1-mediated heat shock response. by Jay Miles, Sarah Townend, Dovilė Milonaitytė, William Smith, Francesca Hodge, David R Westhead, Patricija van Oosten-Hawle

“…Here, we conducted a combinatorial approach using transcriptome RNA-Seq profiling and a forward genetic mutagenesis screen to elucidate how stress signaling from the intestine to the muscle is regulated. …”
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Genome-wide exonic small interference RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum. by Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee

“…Each fungal species appears to have evolved RNAi-based gene regulation for specific developmental stages or stress responses. This study provides new insights into the regulatory role of sRNAs in fungi and other lower eukaryotes.…”
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A chromosomal-level genome assembly of the tropical sea cucumber Stichopus fusiformiossa by Nyok-Sean Lau, Noorizan Miswan, Nurlina Rosli, Sixu Gong, Izzat Irfan, Mathan Ganasan, Sau Pinn Woo, Annette Jaya-Ram

“…This high-quality genome assembly and Iso-Seq transcriptome data provide a valuable resource for advancing genetic and functional studies in S. fusiformiossa, supporting future research into its unique biological traits and potential applications.…”
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Repeated evolution of circadian clock dysregulation in cavefish populations. by Katya L Mack, James B Jaggard, Jenna L Persons, Emma Y Roback, Courtney N Passow, Bethany A Stanhope, Estephany Ferrufino, Dai Tsuchiya, Sarah E Smith, Brian D Slaughter, Johanna Kowalko, Nicolas Rohner, Alex C Keene, Suzanne E McGaugh

“…Together, these findings reveal multiple independent mechanisms for loss of circadian rhythms in cavefish populations and provide a platform for studying how evolved changes in the biological clock can contribute to variation in sleep and circadian behavior.…”
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Development and selection of stably expressed reference genes for expression normalization in Ribes odoratum under drought stress by Jun Xu, Ting Li, Xiaowen Liu, Wenjun Shi, Defang Zhang, Yajun Chang

“…In this study, Through drought stress treatments and transcriptome analysis of Ribes odoratum, this study identified multiple genes with stable expression under drought stress. …”
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Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenance by Alexander S. Ham, Shuo Lin, Alice Tse, Marco Thürkauf, Timothy J. McGowan, Lena Jörin, Filippo Oliveri, Markus A. Rüegg

“…To elucidate how the NMJ transcriptome is regulated, we also performed snRNA-seq on sciatic nerve transected, botulinum toxin injected, and Musk knockout muscles. …”
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An Oct4‐Sall4‐Nanog network controls developmental progression in the pre‐implantation mouse embryo by Meng How Tan, Kin Fai Au, Denise E Leong, Kira Foygel, Wing H Wong, Mylene WM Yao

“…Strikingly, the knockdown embryos arrested at a range of developmental stages. We provided evidence that the DNA methyltransferase Dnmt3b has a role in determining the extent to which a knockdown embryo can develop. …”
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THUMPD3 regulates alternative splicing of ECM transcripts in human lung cancer cells and promotes proliferation and migration. by Marie Klimontova, Han Zhang, Francisco Campos-Laborie, Natalie Webster, Byron Andrews, Kimberley Chung Kim Chung, Ryan Hili, Tony Kouzarides, Andrew J Bannister

“…Overall, these findings highlight THUMPD3 as an important player in regulating cancer-relevant alternative splicing and they provide a rationale for further investigations into THUMPD3 as a candidate target in anti-cancer therapy.…”
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Conditioned Medium Derived From Human Dental Follicle Mesenchymal Stem Cells Alleviates Macrophage Proinflammatory Responses Through MAPK-ERK-EGR1 Axis by Chuhan Zhang, Peiyi Lv, Qiuying Liang, Jian Zhou, Buling Wu, Wenan Xu

“…Elevated EGR1 levels inhibited inflammatory gene expression, inhibiting the pro-inflammatory immunoregulatory function of macrophages in inflammatory states. This study provides an efficient method for in vitro macrophage polarization identification. …”
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