Transcriptomic and proteomic analysis of the jejunum revealed the effects and mechanism of protocatechuic acid on alleviating Salmonella typhimurium infection in chickens by Sheng Zhang, Qin Wang, Xiangtian Yao, Jingjing Dong, Guanhuo Li, Yingan Zang, Shouqun Jiang, Yibing Wang

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Analysis of transcriptome and chromatin accessibility changes during the differentiation of human embryonic stem cells into neural progenitor cells by LI Linying, CAI Xiaodong, TONG Ran, YANG Chen, WANG Zhiming, HE Xiaoyu, MA Ziyue, ZHANG Feng, LI Lingjie, ZHOU Junmei

“…Finally, an integrated analysis of RNA-seq and ATAC-seq data and the protein-protein interaction (PPI) network were performed to identify key genes and regulatory pathways involved in the early stages of neural differentiation in vitro.Results·Both RT-qPCR and IF results indicated that the expression levels of pluripotency markers (NANOG and POU5F1) were high at the hESC stage but significantly decreased at the NPC stage, while early neural differentiation markers (PAX6, SOX1, and NES) were minimally expressed at the hESC stage but markedly upregulated at the NPC stage. …”
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Placental whole transcriptome expression profile in patients with early-onset, late-onset preeclampsia and gestational diabetes mellitus by Zhuo Chen, Li Yang, Li Geng, Xinwen Zhang, Mingyu Du, Yonghu Sun, Lin Zhao, Bing Bai, Xiaohong Li

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Coupling genome-wide continuous perturbation with biosensor screening reveals the potential targets in yeast isopentanol synthesis network by Qi Xiao, Jingjing Shi, Lixian Wang, Guoping Zhao, Yanfei Zhang

“…The F2 strain, in particular, achieved an isopentanol titer of 1.57 ± 0.014 g/L and a yield of 14.04 ± 0.251 mg/g glucose (10% glucose), surpassing the highest values reported to date in engineered Saccharomyces cerevisiae. Systematic transcriptome analysis of the isopentanol synthesis, glycolysis, glycerol metabolism, and ethanol synthesis pathways revealed that MPC, OAC1, BAT2, GUT2, PDC6, and ALD4 are linked to efficient isopentanol production. …”
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Comparative Transcriptomic Analysis Between High- and Low-Growth-Rate Meat-Type Rabbits Reveals Key Pathways Associated with Muscle Development by Chao Yang, Lingxi Zhu, Li Tang, Xiangyu Zhang, Min Lei, Xiaohong Xie, Cuixia Zhang, Dingsheng Yuan, Congyan Li, Ming Zhang

“…The transcriptome analysis showed that 284 and 305 differentially expressed genes (DEGs) (|log2FC| > 1, padj < 0.05) were identified in thigh muscle and <i>longissimus dorsi</i> muscle, respectively. …”
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Aging and head and neck cancer insights from single cell and spatial transcriptomic analyses by Yi Pei, Zhuying Mou, Lai Jiang, Jinyan Yang, Yuheng Gu, Jie Min, Lingyi Sunzhang, Nan Xiong, Xiang Xu, Hao Chi, Ke Xu, Sinian Liu, Huiyan Luo

“…In this research, single cell sequencing and spatial transcriptome analysis were used to investigate the expression of Aging-related genes (ARGs) in HNSCC and to analyse their prognostic significance. …”
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Molecular signatures of preeclampsia subtypes determined through integrated weighted gene co-expression network analysis and differential gene expression analysis of placental tran... by Luhao Han, Fabricio da Silva Costa, Fabricio da Silva Costa, Anthony Perkins, Anthony Perkins, Olivia Holland, Olivia Holland

“…This study aims to use integrated bioinformatics analysis of placental transcriptomics to investigate subtype-specific molecular mechanisms associated with PE.MethodsA systematic search of the Gene Expression Omnibus (GEO) repository identified two datasets (GSE234729, n = 123; GSE75010, n = 157) for integrated Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene expression analysis. …”
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Identification and isolation pipeline for single cell transcriptomic of magnetically enriched tumor cells by Peng Liu, Sitian He, Mette Ø. Agerbæk, Ali Salanti, Leon W.M.M. Terstappen, Pascal Jonkheijm, Michiel Stevens

“…Introduction: The transcriptomic analysis of circulating tumor cells provides valuable insights into cancer metastasis, heterogeneity and the identification of drugable targets. …”
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Identification and validation of differentially expressed genes in allergic asthma pathogenesis using whole-transcriptome sequencing by Fang Cui, Rui Liu, Li Wang, Jing He, Yanxia Xu

“…Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were employed to elucidate the biological significance of the differentially expressed genes, offering insights into the molecular mechanisms underlying allergic asthma.ResultsDifferential expression analysis identified multiple genes with significant differences between the patient and control groups. …”
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Integrative Mendelian randomization and multi-omics analysis identifies anti-allergic drug targets associated with cardiovascular disease risk by Huilin Lian, Dai Li, Youjie Zeng, Yi Meng, Ruifang Chen, Ren Guo

“…Sensitivity analyses, transcriptomics analysis, enrichment analysis, and molecular docking were performed to evaluate the robustness of causality, potential pathways and binding affinity. …”
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Integrated Analysis of Survival, Physiological‐Biochemical, and Transcriptomic Changes Reveals the Impact of Saline Stress on the Freshwater Snail Pomacea canaliculata by Yingtong Chen, Fucheng Yao, Zhaoji Shi, Chunxia Zhang, Jimin Liu, Jiaen Zhang, Zhong Qin

“…Based on transcriptome analysis conducted for the liver and gills of the snails, a total of 1,569,678,584 raw reads were obtained from the nine libraries on the Illumina Novaseq 6000 platform. …”
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PIT-1/SF-1-positive pituitary tumors in patients with acromegaly: transcriptomic perspective by Julia Rymuza, Qilin Zhang, Mateusz Bujko

“…The aim of our study was to clarify their identity and cell type origin using extensive transcriptomic analysis. For this purpose, we analyzed the RNA sequencing (RNAseq) data from 546 PitNETs (including 193 tumors of patient with acromegaly) and single cell RNAseq data from somatotroph and gonadotroph tumors and normal pituitary tissue. …”
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Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) vari... by Guangxia Duan, Chaoni Liang, Jundong Su, Yan Liang, Wanming Li, Jinbo Zhang, Yigong Zhang

“…The salinity tolerance of DY3 was associated with greater biomass, higher antioxidant enzyme activity, and higher photosynthetic efficiency. Transcriptomic analysis revealed that the genes induced in DY3 under salinity stress were associated with ion homeostasis, antioxidant defense system, and plant hormone signaling. …”
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The alteration of IL-17 signaling pathway in bipolar disorder: a preliminary study with transcriptomic perspective by Xiaobo Wang, Xiaobo Wang, Su Yu, Zhen Gao, Fangming Xu, Yumei Wang, Yumei Wang, Yumei Wang, Tianle Zhang, Tingting Xie, Xihua Jia

“…Validation of differentially expressed genes within the IL-17 pathway was conducted through qRT-PCR, while ELISA measured specific protein levels. GO and KEGG pathway enrichment analyses were performed, alongside PPI analysis and Gene Set Variation Analysis (GSVA) to assess immune cell infiltration.ResultsIn the comparison between BD and HC, a total of 304 differentially expressed genes (DEGs) were identified, of which 217 genes were upregulated and 87 genes were downregulated. …”
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Transcriptome and targeted metabolome analysis of lipid profiles, nutrients compositions and volatile compounds in longissimus dorsi of different pig breeds by Zhen Luo, Ting Lai, Yijia Fan, Chengbin Yu, Wei Li, Meng Li, Shenghui Lei, Jing Zhang, Weina Xu, Zhe Wang, Jianxiong Xu

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The Potential Role of GJA1 and SPP1 Expressed by the Endometrium Based on Single Cell Transcriptome Analysis in Endometrial Infertility by Zhenzhen Lu, Qianqian Tang, Chunyan Chen, Xiaojie Zhao, Ying Gao, Qiongqiong Wei

“…Results: Through bioinformatics analysis, we found that the proportion of ciliated cells peaked from the early to mid secretory phase, ciliary motility decreased in the mid secretory phase, while the hub gene that connexin 43 (GJA1) and secreted phosphoprotein 1 (SPP1) expressed in the endometrium may determine successful pregnancy. …”
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Unveiling the molecular mechanism of sepal curvature in Dendrobium Section Spatulata through full-length transcriptome and RNA-seq analysis by Xuefeng Qu, Na Li, Cong Xu, Zifeng Huang, Chunyan Li, Yang Jiang, Guizhao Zheng, Haiping Fu, Guangyan Zhang, Chuan Liu

“…However, the molecular and cellular mechanisms underlying this trait remain poorly understood.MethodsMorphological characteristics of five hybrids were analyzed, with a particular focus on hybrid H5, which exhibits pronounced sepal curling. Full-length transcriptomic sequencing was employed to assemble a reference transcriptome, while RNA-seq identified differentially expressed genes (DEGs) between sepals and petals. …”
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Single-cell and spatial transcriptomics analysis reveals that Pros1+ oligodendrocytes are involved in endogenous neuroprotection after brainstem stroke by Shaojun Li, Guanfeng Zeng, Chunmei Pang, Jie Li, Li Wu, Ming Luo, Zhihua Qiu, Yongjun Jiang

“…Method: A mouse model of brainstem stroke was established, and single-cell RNA sequencing and spatial transcriptomic sequencing analysis were performed to elucidate the phenotype of oligodendrocytes within this context. …”
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Insights into the Metabolite Profiles of Two <i>Camellia</i> (Theaceae) Species in Yunnan Province through Metabolomic and Transcriptomic Analysis by Miao Niu, Ranyang Li, Xiongyu Li, Hongyan Yang, Jianliang Ding, Xianxiu Zhou, Yuqi He, Yawen Xu, Qian Qu, Zhiwei Liu, Jiahua Li

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Investigating potential biomarkers associated with antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis using Mendelian randomization and transcriptomic analysis by Yujia Wang, Zhimin Chen, Kaiqi Huang, Keng Ye, Shiwei He, Yanfang Xu, Hong Chen

“…This study aimed to explore novel biomarkers for AAV through transcriptomic data analysis and Mendelian randomization (MR). …”
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