Human brain single-cell data reveal shared synaptic dysfunction and immune abnormality in epilepsy and Alzheimer′s disease by YU Xiaolin, ZHANG Erning, SHA Longze

“…Methods The single-cell transcriptome sequencing data of brain tissue from AD and epilepsy patients were collected from gene expression omnibus (GEO) database followed by cell clustering, differential expression analysis and gene ontology (GO)functional enrichment analysis using R-based tools such as Seurat and cluster Profiler and video electroencephalogram (vEEG) monitoring and Western blot experiments. …”
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Exploring genetic loci linked to COVID-19 severity and immune response through multi-trait GWAS analyses by Ziang Meng, Chumeng Zhang, Shuai Liu, Wen Li, Yue Wang, Qingyi Zhang, Bichen Peng, Weiyi Ye, Yue Jiang, Yingchao Song, Miao Guo, Xiao Chang, Lei Shao

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Genetic and molecular insights into tiller development and approaches for crop yield improvement by Zaid Chachar, Xiaoming Xue, Junteng Fang, Ming Chen, Weiwei Chen, Xuhui Li, Nazir Ahmed, Sadaruddin Chachar, Aamir Ali, Zhong liang Chen, Lina Fan, Ruiqiang Lai, Yongwen Qi

“…This review offers a comprehensive analysis of recent advancements in enhancing crop yield through extensive research on tiller development, utilizing a multi-faceted approach that includes quantitative trait loci (QTL) mapping, association studies, and transcriptome analysis across various crops. …”
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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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Natural ligand 3,3’-diindolylmethane functions as an AHR agonist to modulate angiogenesis and organ development in chicken embryos by Gee-yea Lim, Hao Chen, Woo-seon Song, Dong-hee Koh, Dong-ha Kim, Hisato Iwata, Eun-Young Kim

“…Further investigations into the effects of DIM were performed through in ovo experiments, transcriptome analysis, and a shell-less incubation system, assessing its impact on chicken embryo development. …”
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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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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

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Multi-omics profiling reveals distinct pathogenic mechanisms in Hunner and non-Hunner interstitial cystitis subtypes by Lin Zhu, Hanwei Ke, Qi Wang, Kexin Xu, Xiaofang Chen

“…This study aims to delineate the differences between NHIC and HIC using multi-omics analysis to uncover distinct microbiome, metabolome, and transcriptome profiles, thereby elucidating their unique pathogenic mechanisms. …”
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Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds by Suthar Teerath Kumar, Yunlong Zheng, Jing Xu, Ziyi Zhao, Qi Zhang, Yunpeng Zhang, Min Li, Hong Zou, Riaz Muhammad Azeem, Wu-Sheng Sun, Yuan Zhao, Shu-Min Zhang

“…Transcriptome analysis identified 134 upregulated and 362 downregulated genes in the SBP. …”
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Combined metabolome and transcriptome to analyze the regulatory network of key enzymes in the synthesis of senkirkine in Emilia sonchifolia by Jinli Yao, Yanqing Qin, Dongping Tu, Yumei Huang, Liuguan Liang, Wenhui Cai, Mingli Huang, Xiaoqi Zhu, Xinling Lao

“…Senkirkine showed the most significant content variation between roots and flowers, with roots containing notably higher levels. Transcriptomic analysis identified 119,886 unigenes and 32,797 DEGs. …”
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Identifying candidate genes associated with hippocampal dysfunction in a hemiparkinsonian rat model by transcriptomic profiling by Bohye Kim, Sungmoo Hong, Jeongmin Lee, Sohi Kang, Joong-Sun Kim, Chaeyong Jung, Taekyun Shin, BuHyun Youn, Changjong Moon

“…RNA sequencing and gene expression analysis unveiled 1018 DEGs in the ipsilateral rat hippocampus following 6-OHDA infusion: 631 genes exhibited upregulation, while 387 genes were downregulated (with FDR-adjusted p-value < 0.05 and absolute fold-change > 1.5). …”
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Bronchoalveolar lavage single-cell transcriptomics reveals immune dysregulations driving COVID-19 severity. by Clinton Njinju Asaba, Razieh Bitazar, Patrick Labonté, Terence Ndonyi Bukong

“…Using single-cell transcriptomics, we conducted a secondary data analysis of bronchoalveolar lavage fluid (BALF) from COVID-19 patients of varying severities and healthy controls to comprehensively examine immune responses. …”
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The spatial transcriptome of the late-stage embryonic and postnatal mouse brain reveals spatiotemporal molecular markers by Yuichiro Hara, Takuma Kumamoto, Naoko Yoshizawa-Sugata, Kumiko Hirai, Xianghe Song, Hideya Kawaji, Chiaki Ohtaka-Maruyama

“…However, markers established in the adult brain sometimes behave differently in the fetal brain, actively changing during development. The spatial transcriptome is a powerful analytical method that enables sequence analysis while retaining spatial information. …”
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Integrated transcriptomics of multiple sclerosis peripheral blood mononuclear cells explored potential biomarkers for the disease by Arman Mokaram Doust Delkhah

“…After implementing weighted gene co-expression network analysis (WGCNA) and discovering MS-specific modules, the converging results of differential expression analysis and WGCNA were subjected to machine learning methods. …”
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Identifying KLF14 as a potential regulatory factor in liver regeneration trough transcriptomic and metabolomic by Chang Liu, Dalong Zhu, Junlong Xue, Alimu Tulahong, Tuerganaili Aji

“…Peripheral blood samples were collected from three patients undergoing PH and three patients undergoing ELRA at three time points: pre-operation, postoperative day 1, and postoperative day 5, as well as three healthy controls. Transcriptomic analysis was performed to identify differentially expressed genes (DEGs) using RNA sequencing, while metabolomic analysis was conducted using untargeted liquid chromatography-mass spectrometry (LC–MS). …”
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Transcriptomics Revealed Differentially Expressed Transcription Factors and MicroRNAs in Human Diabetic Foot Ulcers by Vikrant Rai

“…The analysis revealed 30 differentially expressed transcription factors (21 activated and 9 inhibited), two translational regulators (RPSA and EIF4G2), and seven miRs, including mir-486, mir-324, mir-23, mir-186, mir-210, mir-199, and mir-338 in upstream regulators (<i>p</i> < 0.05), while causal network analysis (<i>p</i> < 0.05) revealed 28 differentially expressed TFs (19 activated and 9 inhibited), two translational regulators (RPSA and EIF4G2), and five miRs including mir-155, mir-486, mir-324, mir-210, and mir-1225. …”
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Molecular mechanisms after optic nerve injury: Neurorepair strategies from a transcriptomic perspective by Xiaxue Chen, Muyang Wei, Guangyu Li

“…This review focuses on optic nerve crush and glaucoma models, elucidating the mechanisms of optic nerve injury and neuron degeneration induced by glaucoma through single-cell transcriptomics, transcriptome analysis, and chip analysis. …”
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Identification of ligand and receptor interactions in CKD and MASH through the integration of single cell and spatial transcriptomics. by Jaime Moreno, Lise Lotte Gluud, Elisabeth D Galsgaard, Henning Hvid, Gianluca Mazzoni, Vivek Das

“…To achieve this, we created an integrative analysis framework in CKD and MASH from two available human cohorts.…”
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Single-cell transcriptomics reveals metabolic remodeling and functional specialization in the immune microenvironment of bone tumors by Jun Chen, Na Cui, Shao-Hui He, Chun-Yan Xia, Wei-Qing Li

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Physiological and Transcriptome Analyses of Gill and Hepatopancreas of <i>Potamocorbula ustulata</i> Under Ammonia Exposure by Jing He, Xinhui Wang, Mingyu Wu, Zhihua Lin, Lin He, Xiafei Zheng

“…Antioxidant enzyme activity was significantly altered in the gills and hepatopancreas, with GS, GDH, and ARG levels markedly increasing in the hepatopancreas. Transcriptome analysis revealed that after 24 h of exposure, differentially expressed genes (DEGs) were enriched in apoptosis and inflammation-related pathways (MAPK, NF-kB, NOD-like receptor signaling). …”
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