RNA-Seq transcriptome profiling reveals distinct immune response landscapes to identifying inflammation-related diagnostic markers in latent endometrial tuberculosis by Bai Dai, Jing-ying Liu, De-Bang Li, Zhi-ming Wang, Xiu-juan Chen

“…Our study included clinical diagnostics, histological examinations, and transcriptomic analyses comparing differentially expressed genes (DEGs) among control, LETB, and active TB groups. …”
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GC-MS metabolite and transcriptome analyses reveal the differences of volatile synthesis and gene expression profiling between two Chinese rose cultivars by Kaiqing Luo, Chao Song, Tingting Bao, Rui Huang, Shengnan Lin, Yingxue Yang, Luhong Leng, Xuezhu Liao, Cuihua Gu, Zhiqiang Wu, Xiaoni Zhang

“…This study conducted metabolomic and transcriptomic analyses on the floral volatile compounds of Rosa chinensis (R. chinensis) 'Old Blush' ('OB') and R. chinensis 'Chilong Hanzhu' ('CH'). …”
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Maternal e-cigarette exposure alters DNA methylome, site-specific CpG and CH methylation, and transcriptomic signatures in the neonatal brain by Andrew Walayat, Maryam Hosseini, Chirag Nepal, Yong Li, Wanqiu Chen, Zhong Chen, Xiaohui Huang, Xuesi M. Shao, Lubo Zhang, Charles Wang, Daliao Xiao

“…This study aimed to understand the effects of fetal e-cig exposure on DNA methylome and transcriptomic changes in the neonatal brain. Pregnant rats were exposed to e-cig aerosols, and neonatal brains (5 males and 5 females/group) from both control and e-cig-exposed groups were used for experimental analysis. …”
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Comparative Analysis of Digital Transcriptomics Between Pre- and Post-Treatment Samples of Patients with Locally Advanced Cervical Cancer: A Preliminary Study by Sunhwa Baek, Fabian Dominik Mairinger, Sabrina Borchert, Yue Zhao, Dominik Ratiu, Peter Konrad Mallmann, Henryk Pilch, Ka-Won Noh

“…This study aimed to explore the transcriptomic changes associated with the therapeutic response in locally advanced cervical cancer, focusing on 770 immune-related genes. …”
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Global analysis of transcriptome and metabolomics revealed that fatty acid synthesis and urea cycle process regulate the growth of chinese soft-shelled turtle by Tong Zhou, Guobin Chen, Lihuan Cao, Jizeng Cao, Huizi Ji, Guiwei Zou, Hongwei Liang

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Integrative transcriptomic and single-cell analysis reveals IL27RA as a key immune regulator and therapeutic indicator in breast cancer by Yi Chen, Munawar Anwar, Xiaoli Wang, Boxiang Zhang, Binlin Ma

“…Conclusion IL27RA is a potential immune biomarker that reflects an inflamed tumor microenvironment and predicts benefit from immunotherapy and chemotherapy in breast cancer. These findings provide novel insights into immune-based stratification using single-cell transcriptomic data.…”
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Integrated meta‐QTL and in silico transcriptome assessment pinpoint major genomic regions responsible for spike length in wheat (Triticum aestivum L.) by Changgang Yang, Xueting Zhang, Shihong Wang, Na Liu

“…Integration of MQTL analysis and in silico transcriptome data led to a significant increase in the reliability of CGs for the genetic regulation of wheat SL, and the haplotype analysis for key CGs TaPP2C‐3B of SL provided insights into the biological function of the TaPP2C‐3B gene.…”
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Combined Analysis of Transcriptomes and Metabolomes Reveals Key Genes and Substances That Affect the Formation of a Multi-Species Biofilm by Nine Gut Bacteria by Ting Zhang, Zhangming Pei, Hongchao Wang, Jianxin Zhao, Wei Chen, Wenwei Lu

“…The combined analysis of the transcriptomes and metabolomes showed that there were 26 common DEGs highly correlated with the four common DAMs, and they were involved in five metabolic pathways related to amino acids and purines. …”
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Transcriptome analysis of Aspergillus oryzae RIB40 under chemical stress reveals mechanisms of adaptation to fungistatic compounds of lignocellulosic side streams by Miika-Erik Korpioja, Emmi Sveholm, Adiphol Dilokpimol, Tanja Paasela, Andriy Kovalchuk

“…In the present study, the cellular mechanisms of tolerance against furfural, 5-hydroxymethylfurfural (HMF), levulinic acid, ferulic acid, and vanillin were studied at the transcriptome level. Results A. oryzae RIB40 was grown in the presence of different inhibitors commonly found in lignocellulosic side streams, and RNA sequencing was utilized to investigate the transcriptomic changes in response to the inhibitors. …”
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Comprehensive GWAS and Transcriptome Analysis Discovered Candidate Gene Associated with Starch Pasting Properties of Temperate japonica rice (Oryza sativa L.) by Yoon Kyung Lee, Su Jang, Jihwan Im, Hee-Jong Koh

“…LD block analysis and transcriptome analysis of accessions with extreme phenotypes identified OsGLUTN (Os02g0224300/LOC_Os02g13130), a gene encoding a high molecular weight glutenin subunit-like protein, as a strong candidate. …”
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Dynamic metabolomic and transcriptomic profiling reveals yellow flower development in Camellia perpetua, a rare continuously flowering golden Camellia species by Xianliang Zhu, Haidu Jiang, Xinfeng Pan, Jiaxin Fu, Lihui Peng, Jin Zhang, Jianmin Tang, Rong Zou, Bo Zhao, Xiao Wei, Shengfeng Chai

“…To investigate the dynamics of metabolite accumulation and gene expression during the yellow flower formation of C. perpetua, a continuously flowering golden camellia, a comprehensive metabolomic and transcriptomic analysis was performed across five distinct developmental stages. …”
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Single-cell transcriptomics reveals BMP4-BMPR2 signaling promotes radiation resistance in hematopoietic stem cells following injury by Yanhua Li, Yunxing Li, Bowen Zhang, Jiahui Zhao, Jinhua Qin, Siao Jiang, Yunqiao Li, Yanzhou Chen, Jisheng Li, Keyi Chen, Yang Lv, Tao Fan, Zuyin Yu, Hao Lu, Cheng Quan, Yiming Lu, Xuetao Pei, Gangqiao Zhou

“…Here, we present a dynamic single cell transcriptomic landscape and elucidate the complex crosstalk between HSPCs and the bone marrow (BM) microenvironment during IR-induced regeneration process. …”
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Comparative Transcriptome Analysis Reveals the Impact of a High-Fat Diet on Hepatic Metabolic Function in Tilapia (<i>Oreochromis niloticus</i>) by Rui Jia, Yiran Hou, Linjun Zhou, Liqiang Zhang, Bing Li, Jian Zhu

“…This study aimed to assess changes in hepatic metabolic function in tilapia and to explore the underlying molecular mechanisms through transcriptomic analyses. Tilapia were allocated into two groups: a normal control (Ctr)-fed group and a high-fat diet (HFD)-fed group. …”
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Causal association of immune-related genes with mouth ulcers: findings from summary-based Mendelian randomization and transcriptome-wide association analysis by Mengru Shi, Tianqi Wang, Qi Xie, Guangwei Yuan, Juan Xia, Jingyun Yang, Weili Xie, Zetao Chen, Xiaobing Chen

“…This integrative approach provides insights into potential therapeutic targets and advances our understanding of the genetic basis underlying this prevalent condition.…”
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Transcriptomic Profiling of Thermotolerant <i>Sarcomyxa edulis</i> PQ650759 Reveals the Key Genes and Pathways During Fruiting Body Formation by Zitong Liu, Minglei Li, Hongyu Ma, Fei Wang, Lei Shi, Jinhe Wang, Chunge Sheng, Peng Zhang, Haiyang Yu, Jing Zhao, Yanfeng Wang

“…Quantitative PCR validation confirmed the reliability of transcriptome data, with expression trends consistent across both methods. …”
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Combined Physiological and Transcriptomic Analysis Reveals Key Regulatory Networks and Potential Hub Genes Controlling Chilling Tolerance During Soybean Germination by Jianguo Xie, Yuhong Zheng, Guang Li, Wei Zhang, Fanfan Meng, Xuhong Fan, Xingmiao Sun, Yunfeng Zhang, Mingliang Wang, Qingshan Chen, Shuming Wang, Hongwei Jiang

“…Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes enrichment were performed on the differentially expressed genes obtained by transcriptome sequencing. It was found that terms or pathways related to flavonoids, unsaturated fatty acids, and abscisic acid were highly enriched. …”
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Transcriptomic features of immune inflammation and neural plasticity associated with early neurological improvement in acute ischemic stroke patients with large vessel occlusion by Dong Zhang, Xinying Jing, Ruinan Ma, Zhizhang Li, Xiaoguang Zhang, Ying Ding, Yunhua Yue

“…Peripheral blood samples were collected before reperfusion therapy for mRNA transcriptome sequencing and bioinformatic analysis. …”
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Identification of Potential Key Genes for Stem Polysaccharide Synthesis Based on Transcriptome Analysis of Different Developmental Stages of <i>Dendrobium officinale</i> by Tianwei Yang, Shiyu Huang, Shanshan Tian, Manrong Gao, Xiangjun Zhang, Longfei He, Shangwen Zhang

“…To systematically analyze the biosynthetic pathways of polysaccharides and identify key genes involved in polysaccharide synthesis, this research assessed the water-soluble polysaccharide content and conducted transcriptome sequencing on stem tissues of <i>D. officinale</i> at different developmental stages. …”
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Elucidating the causal associations and mechanisms between circulating immune cells and idiopathic pulmonary fibrosis: new insights from Mendelian randomization and transcriptomics by Han Yang, Xuanyu Wu, Xiang Xiao, Jiajing Chen, Xiaomin Yu, Wen Zhao, Fei Wang

“…Subsequently, SNP-nearest genes combined with the transcriptomics data of IPF were subjected to multiple bioinformatics analyses such as TIMER, WGCNA, functional enrichment analysis, protein-protein interaction analysis, and ROC to identify IPF biomarkers. …”
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Comparative metabolome and transcriptome revealed the CpODO1 transcription factor controlling the varied floral scent traits of three wintersweet cultivars by Yubing Yong, Qi Zhou, Xin Ding, Jianming Cheng, Chengcheng Zhou, Zhiguo Shen, Lin Zhang

“…Integrated analyses of metabolome and transcriptome showed that an R2R3-MYB transcription factor gene, CpODO1, potentially have a crucial regulatory function in controlling the production of multiple aroma compounds. …”
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