Depot-specific metabolic and inflammatory profiles in perirenal and renal sinus adipose tissue by Maria J. Pereira, Argyri Mathioudaki, Susanne Hetty, Amir Sedigh, Jan W. Eriksson, Maria K. Svensson

“…Of 1113 significantly differentially expressed genes (DEGs) (PRAT: 571 down- and 542 upregulated), thermogenic and metabolic genes (UCP1, CIDEA, and CKMT1B) were enriched in PRAT, while inflammation-related genes (NFKBIA, BIRC3, and IRF1) in RSAT. …”
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The role of cytokine licensing in shaping the therapeutic potential of wharton’s jelly MSCs: metabolic shift towards immunomodulation at the expense of differentiation by Olena Rogulska, Eliska Vavrinova, Irena Vackova, Jarmila Havelkova, Klara Gotvaldova, Pavel Abaffy, Sarka Kubinova, Michal Sima, Pavel Rossner, Lucie Bacakova, Pavla Jendelova, Katarina Smolkova, Yuriy Petrenko

“…In this study, we evaluated the transcriptomic, metabolomic, and functional changes induced by short-term TNF-α/IFN-γ priming of Wharton’s jelly-derived MSCs (WJ-MSCs). …”
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Transcriptional and neurotransmitter signatures of cerebral spontaneous neural activity in nurses with burnout by Chun-Mei Song, Chun-Mei Song, Jian-Ping Liu, Hu-Cheng Yang, Qing-He Li, Shu Wang, Hai-Juan Chen, Shu-Fang Wang, Li Chen, Si-Yu Gu, Feng Zhang, Ping-Lei Pan

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Gibberellin-induced germination enhancement in Chinese sour jujube seeds under cold stress by Qiang Chen, Guolong Li, Jinao Duan, Zhishu Tang, Zhongxing Song, Hongbo Liu, Xinbo Shi

“…Comprehensive metabolomics and transcriptomics analysis showed that phenylpropionic acid/zeatin biosynthesis gene (4CL, CCR) was up-regulated, while CKX and PAL were down-regulated, which were related to the increase of zeatin and the decrease of abscisic acid metabolites. …”
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A scRNA-seq reference contrasting living and early post-mortem human retina across diverse donor states by Luning Yang, Yiwen Tao, Qi Pan, Tengda Cai, Yunyan Ye, Jianhui Liu, Yang Zhou, Yongqing Shao, Quanyong Yi, Zen Huat Lu, Lie Chen, Gareth McKay, Richard Rankin, Weihua Meng

“…After standardized dissociation, single-cell transcriptomes were generated using 10x Genomics 3’ RNA-seq and applied scVI to generate batch-corrected integrated atlas. …”
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Evidence for trans-generational immune priming against Vibrio splendidus in the oyster Crassostrea gigas by Xiaorui Song, Xiaorui Song, Weilin Wang, Weilin Wang, Weilin Wang, Miren Dong, Miren Dong, Miren Dong, Chang Liu, Chang Liu, Chang Liu, Chuanyan Yang, Chuanyan Yang, Chuanyan Yang, Lingling Wang, Lingling Wang, Lingling Wang, Linsheng Song, Linsheng Song, Linsheng Song

“…Transcriptome data revealed that differentially expressed genes were enriched in immunity, signal transduction, energy metabolism, and development in the parental TGIP groups. …”
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Deciphering the Oncogenic Landscape of Hepatocytes Through Integrated Single‐Nucleus and Bulk RNA‐Seq of Hepatocellular Carcinoma by Huanhou Su, Xuewen Zhou, Guanchuan Lin, Chaochao Luo, Wei Meng, Cui Lv, Yuting Chen, Zebin Wen, Xu Li, Yongzhang Wu, Changtai Xiao, Jian Yang, Jiameng Lu, Xingguang Luo, Yan Chen, Paul KH Tam, Chuanjiang Li, Haitao Sun, Xinghua Pan

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Omics data integration analysis identified new biological insights into chronic antibody-mediated rejection (CAMR) by Maurizio Bruschi, Simona Granata, Francesca Leone, Laura Barberio, Giovanni Candiano, Paola Pontrelli, Andrea Petretto, Martina Bartolucci, Sonia Spinelli, Loreto Gesualdo, Gianluigi Zaza

“…CHI3L1, previously associated with the severity of tissue damage in kidney diseases, was up-regulated in CAMR in both transcriptomics and proteomics, while SERPING1, a serine esterase inhibitor that blocks the classical and lectin pathway of complement, was up-regulated in CAMR in transcriptomics but down-regulated in proteomics. …”
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Neuroprotective effects of ethanol extraction from Rubia yunnanensis Diels on chronic cerebral hypoperfusion: modulation of the System Xc-/GSH/GPX4 axis to alleviate oxidative stre... by Jianghao Cheng, Xiaoxia Ma, Jie Tao, Xiaoli Jiang, Pu Chen, Xiaohua Duan

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Ocean acidification induces changes in circadian alternative splicing profiles in a coral reef fish by Sneha Suresh, Michael Jarrold, Timothy Ravasi, Philip L. Munday, Celia Schunter

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Comprehensive characterization of NK cell-related genes in cutaneous melanoma identified a novel prognostic signature for predicting the prognosis, immunotherapy, and chemotherapy... by Haili Ma, Jian Liu, Huan Jin, Min Zhang, Qian Liang, Zhiqiang Guo

“…Single-cell transcriptomes from CM were analyzed in conjunction with immune genes to identify NKIGs. …”
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Impact of SARS-CoV-2 Variant NSP6 on Pathogenicity: Genetic Analysis and Cell Biology by Yangye Gao, Peng Ni, Yanqiao Hua, Shuaiyin Chen, Rongguang Zhang

“…This study investigated the structural and functional impacts of NSP6 mutations by analyzing NSP6 proteins from the Wuhan-Hu-1/B (WT) strain and predominant variants Alpha, XBB.1.16, BA.2.86, and JN.1 using bioinformatics, transcriptomics, and cellular experiments. The results demonstrate that the V3593F mutation decreased the β-sheet proportion and modified hydrogen bonding patterns, while the L3829F mutation enhanced structural stability by promoting random coils. …”
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Resiquimod induces a mixed Th1 and Th2 response via STAT1 and STAT3 signalling in chickens by Deepthi Kappala, Saravanan Ramakrishnan, Patel Nikunjkumar Prakashbhai, Abinaya Kaliappan, Prasad Thomas, Jörg Linde, Mithilesh Singh, Sohini Dey, Madhan Mohan Chellappa

“…SB202190, IC-87114, and fludarabine phosphate suppressed the R-848-induced expression of MAPK14, PIK3CD, and STAT1, respectively, while chloroquine decreased STAT3 expression. Intriguingly, chloroquine treatment enhanced the R-848-mediated expression of MAPK11, LRRK2, and GATA3. …”
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The role of JPT1 in hepatocellular carcinoma: tumor progression, microtubule dynamics regulation, and potential mechanisms within the immune microenvironment by Yipin Lu, Peng Xu, Sha Li, Jie Yao

“…Kaplan-Meier survival analysis and Cox proportional hazard models were employed to assess the prognostic potential of JPT1, while a nomogram was constructed to predict 1-, 3-, and 5-year survival rates in HCC patients. …”
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Molecular Mechanism During Mycelium Subculture Degeneration of <i>Volvariella volvacea</i> by Lidan Feng, Lujuan Wang, Yuanxi Lei, Jie Li, Fengyun Zhao

“…There were 245 differentially expressed genes between the M1–M5 and M0 strains, while the highest number of differentially expressed genes was between M3 and M0, at 1439; the smallest number of differentially expressed genes was between M2 and M0, at 959. …”
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Pulsed Electric Field Treatment Modulates Gene Expression and Stress Responses in Fusarium-Infected Malting Barley by Pavel Svoboda, Jaroslava Ovesná, Štěpán Helmer, Milena Stránská

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Investigation of the therapeutic effects and mechanisms of Houpo Mahuang Decoction on a mouse model of chronic obstructive pulmonary disease by Shanlan Li, Ziqi Dai, Tong Zhang, Zhuoqian Guo, Feng Gao, Xuehao Cheng, Jin An, Yixuan Lin, Xiaomin Xiong, Nan Wang, Guanghui Jiang, Bing Xu, Haimin Lei

“…Network pharmacology and transcriptomics further revealed the mechanism, indicating that the IL-17 signaling pathway might been instrumental in the inhibitory effect of HPMHD on mouse model of COPD. …”
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Integrative genomic analysis identifies novel causal genes of Hodgkin’s and non-Hodgkin’s lymphoma by Patrick Shi, Ancha Baranova, Hongbao Cao

“…Key genes that influence NHL risk include KRT1, ERAP2, RMDN1, FAS, and C5, while UNC5B was identified as a significant causal gene for HL. …”
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Multi-omics analysis of the mechanisms of abundant theacrine and EGCG3"Me in tea (Camellia sinensis) by Yanyu Zhu, Mengya Gu, Wentao Yu, Longhua Liao, Shuilian Gao, Shuyan Wang, Hongzheng Lin, Wenjing Gui, Youliang Zhou, Zhiming Chen, Jingde Zeng, Naixing Ye

“…Through integrated transcriptome-proteome-metabolome analysis, SAMS3, APRT1, IMPDH, and TCS1 were identified as critical enzymes for theacrine synthesis; while CHI1, CHI2, FLS2 and LAR1 were key for EGCG3"Me synthesis. …”
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GeNetFormer: Transformer-Based Framework for Gene Expression Prediction in Breast Cancer by Oumeima Thaalbi, Moulay A. Akhloufi

“…This dataset contains 68 H&E-stained histology images and transcriptomics data from different types of breast cancer. …”
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