Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding by I. V. Bykova, N. A. Shmakov, D. A. Afonnikov, A. V. Kochetov, E. K. Khlestkina

“…This information should prove useful while planning comparative assays of potato transcriptome or application of DNA-markers. …”
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Integrated multi-omics analysis identifies lipid metabolism biomarkers in ONFH and reveals therapeutic potential of retinoic acid by Chuan Wang, Chaode Cen, Huachuan Su, Yuhui Peng, Tao Wang, Jian Li, Fei Zhang, Wuxun Peng

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A comprehensive transcriptional profiling of developing gonads reveals the role of TGFβ signaling in female gonadal asymmetry in chickens by Hong Jo Lee, Jeong Hoon Han, Brittany Chapman, Kyung Min Jung, Isabella Rudd, Jae Yong Han, Tae Hyun Kim

“…In chickens, the left gonad of female embryos develops into a functional ovary, while the right gonad undergoes degeneration during embryogenesis. …”
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Integrated Transcriptomic and Metabolomic Analyses Reveal the Positive Effects of 5-Aminolevulinic Acid (ALA) on Shading Stress in Peanut (<i>Arachis hypogaea</i> L.) by Qi Wu, Liyu Yang, Haiyan Liang, Miao Liu, Dianxu Chen, Pu Shen

“…To address this, field experiments were designed involving two shading conditions (CK and AS0, no shading; S40 and AS40, 40% shading) and two ALA foliar sprayed levels (CK and S40, no ALA application; AS0 and AS40, 20 mg L⁻¹ (0.15 mM) ALA application) to investigate the effects of the exogenous application of ALA under shading stress via the evaluation of both transcriptome and metabolome. The research results suggested that the exogenous ALA application under normal light conditions significantly enhanced photosynthesis, while exogenous ALA application could improve the stability of the cell membrane structure and biological function in response to shading stress and thereby enhance shading tolerance of the plant. …”
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Integrated Volatile Compounds and Transcriptional Gene Analysis Elucidate the Deterioration Mechanism of Embryo Rice During Storage by Xiyuan Yang, Tingting Su, Lixue Ma, Xindi Mu, Hui Wang, Lei Xu, Lidong Wang, Baijun Wang, Di Yao, Changyuan Wang

“…At the same time, volatile compound analysis and transcriptomic analysis were integrated to explore the quality deterioration mechanism of embryo rice during storage. …”
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Optimal Vase Solution for <i>Gerbera hybrida</i> Cut Flower Keeping Fresh by Activating SA and Cytokinin Signaling and Scavenging Reactive Oxygen Species by Chaoshui Xia, Yiyang Cao, Weixin Gan, Huifeng Lin, Huayang Li, Fazhuang Lin, Zhenhong Lu, Weiting Chen

“…The qRT-PCR analysis of key candidate genes supported these findings, with significant upregulation observed in genes related to cytokinin synthesis (e.g., <i>GhIPT1</i> and <i>GhIPT9</i>), salicylic acid signaling related to pathogen defense (e.g., <i>GhTGA1</i>, <i>GhTGA4</i>, <i>GhNPR1</i>, and <i>GhRBOHA</i>), and plant wax synthesis and stress response (e.g., <i>GhKCS5</i>, <i>GhCUT1</i>, and <i>GhKCS6</i>). Further, transcriptome GO-enrichment and physiological analysis showed that the OS might extend VL of Gerbera cut flowers by scavenging reactive oxygen species, including by activating the expression of genes related to oxidoreductase activity and the activities of antioxidant-system-related enzymes catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX), and superoxide dismutase (SOD), while decreasing the malondialdehyde (MDA) content. …”
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Single-cell sequencing and spatial transcriptomics reveal the evolution of glucose metabolism in hepatocellular carcinoma and identify G6PD as a potential therapeutic target by Deyang Xi, Deyang Xi, Yinshuang Yang, Jiayi Guo, Jiayi Guo, Mengjiao Wang, Mengjiao Wang, Xuebing Yan, Chunyang Li

“…Pseudotime analysis was performed on the single-cell data, while ST data was used to analyze spatial metabolic activity. …”
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Integrating whole-genome re-sequencing and transcriptome data to reveal the molecular mechanism of TBX5 gene regulating feathered feet in Guangxi native chickens by Zhuliang Yang, Yongcui Liu, Jintang Luo, Cong Xiao, Hong Yuan, Wenya Du, Xiurong Yang

“…This study combined whole-genome re-sequencing (WGS) data, transcriptomic analysis, and cellular experiments to investigate the genetic basis of feathered feet in Guangxi native chickens. …”
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Metabolite differences and molecular mechanism between dehiscent and indehiscent capsule of mature sesame by Yinping Zhang, Ruirui Chen, Yujun Liu, Shuwen Xu, Shuguang Gao, Haiyang Zhang, Hongmei Miao, Lingling Qin, Xiangyu Zhou, Kiran Thakur, Cheng Li, Juan Li, Pengcheng Wei, Zhao-Jun Wei

“…Apart from its function in cell signaling, the latter may contribute to the glycosylation of lignin monomers, while the former may provide ATP for cellular microtubule movement. …”
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Multi-omics analysis of methylmalonic acidemia caused by a non-coding region variant in MMAA gene combined with uniparental disomy by HUO Xiaoyan, LUO Xiaomei, YE Xiantao, SUN Yu, YU Yongguo, LIANG Lili, FAN Yanjie

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High spatial resolution gene expression profiling and characterization of neuroblasts migrating in the peri-injured cortex using photo-isolation chemistry by Takuya Miyamoto, Kazuya Kuboyama, Mizuki Honda, Mizuki Honda, Yasuyuki Ohkawa, Shinya Oki, Shinya Oki, Kazunobu Sawamoto, Kazunobu Sawamoto

“…Gene Ontology analysis revealed that in neuroblasts migrating in the peri-injured cortex, expression of genes involved in regulating migration direction and preventing cell death was upregulated, while the expression of genes involved in cell proliferation and maintenance of the immature state was downregulated. …”
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Park7 deletion leads to sex-specific transcriptome changes involving NRF2-CYP1B1 axis in mouse midbrain astrocytes by Sergio Helgueta, Tony Heurtaux, Alessia Sciortino, Yujuan Gui, Jochen Ohnmacht, Pauline Mencke, Ibrahim Boussaad, Rashi Halder, Pierre Garcia, Rejko Krüger, Michel Mittelbronn, Manuel Buttini, Thomas Sauter, Lasse Sinkkonen

“…While at 3 months the transcriptomes of both male and female mice were unchanged compared to their wildtype littermates, an extensive deregulation was observed in 8 month-old males. …”
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Physiological and molecular responses of juvenile silver crucian carp (Carassius gibelio) to long-term high alkaline stress: Growth performance, histopathology, and transcriptomic... by Kemeng Jiang, Wenqian Wang, Jianlin Li, Wenrong Feng, Ezra Martini Kamunga, Zhihua Zhang, Yongkai Tang

“…Genes related to carbohydrate metabolism were upregulated while those related to protein metabolism were downregulated, indicating that alkaline stress caused the organism to utilize carbohydrates rather than proteins as much as possible to meet enhanced metabolism. …”
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Evaluation of Drought Tolerance and Trehalose Response in <i>Auricularia heimuer</i> by Jian Sun, Fangjie Yao, Lixin Lu, Youmin Zhang, Ming Fang, Xiaoxu Ma, Kaisheng Shao, Xu Sun

“…We selected 13 strains of <i>A. heimuer</i> and simulated drought stress using a complete yeast medium (CYM) containing 20% polyethylene glycol (PEG), while the medium used for the control treatments did not contain PEG. …”
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Adaptive Responses of Large Yellow Croaker <i>Larimichthys crocea</i> to Ocean Acidification: Integrative Analysis of Gill and Kidney Transcriptomics and Antioxidant Enzyme Activit... by Ting Ye, Xiaoyan Zhang, Feng Liu, Xiao Liang, Dandan Guo, Bao Lou, Zhigang Xie

“…These findings suggested that the gills play a critical role in adapting to low pH in <i>L. crocea</i>, while the kidneys were more responsive to high pH. …”
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Age-linked DNA methylation and gene expression patterns in parameningeal head and neck alveolar rhabdomyosarcoma reveal CDK9 as a promising therapeutic target by Sara Patrizi, Silvia Vallese, Sabina Barresi, Matteo Cassandri, Isabella Giovannoni, Lucia Pedace, Luana Abballe, Flavia Vinciarelli, Celeste Antonacci, Alessandra Stracuzzi, Barbara Mancini, Ida Russo, Angela Di Giannatale, Rossella Rota, Rita Alaggio, Franco Locatelli, Giuseppe Maria Milano, Evelina Miele

“…Results: DNAm profiles did not significantly differ across age groups, while gene expression was the primary driver of observed differences. …”
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Transcriptome analysis reveals potential regulatory mechanism of genes and pathways following Aeromonas veronii infection and hypoxic stress in Chinese mitten crab, Eriocheir sinen... by Gang Jiang, Fengyuan Yan, Yuanfeng Xu, Jianlin Li, Wenrong Feng, Guo an Hua, Wen jing Li, Jun Zhou, Yongkai Tang

“…Hypoxia activated genes involved in energy metabolism while down-regulated those related to protein synthesis. …”
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Dietary Tannic Acid Promotes Growth Performance and Resistance Against <i>Aeromonas hydrophila</i> Infection by Improving the Antioxidative Capacity and Intestinal Health in the Ch... by Liqin Ji, Yisen Shangguan, Chen Chen, Chengqing Wei, Junxian Zhu, Xiaoyou Hong, Xiaoli Liu, Xinping Zhu, Wei Li

“…Additionally, 1–4 g/kg of TA improved the T-SOD, CAT, and GSH-Px activities during infection, while 2 g/kg of dietary TA enhanced the richness and diversity of the microbiota, for example, by increasing Actinobacteria but inhibiting Firmicutes. …”
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Methylation and gene expression patterns in adamantinomatous craniopharyngioma highlight a panel of genes associated with disease progression-free survival by Junier Marrero-Gutiérrez, Ana Carolina Bueno, Ana Carolina Bueno, Clarissa Silva Martins, Rui Milton Patrício Silva-Júnior, Antônio Carlos dos Santos, Marcelo Volpon Santos, Luiz Eduardo Wildemberg, Ximene Lima da Silva Antunes, Monica R. Gadelha, Ayrton Custodio Moreira, Ricardo Zorzetto Nicoliello Vêncio, Sonir Roberto R. Antonini, Margaret de Castro

“…While most clinical and histopathological characteristics were similar between clusters, ACP-A exhibited a longer median progression-free survival. …”
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Transcriptome Profiling Unveils the Mechanisms of Inflammation, Apoptosis, and Fibrosis in the Liver of Juvenile Largemouth Bass <i>Micropterus salmoides</i> Fed High-Starch Diets by Xifeng Liu, Hongkang Liu, Kangwei Wang, Chuanjie Qin, Yuanfa He, Li Luo, Shimei Lin, Yongjun Chen

“…Histological evaluation of the livers showed that vacuolization was the most prevalent characteristic in the MS fish, while ballooning degeneration, apoptosis, fibrosis, and inflammation were observed in the HS fish. …”
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