Molecular landscape of atherosclerotic plaque progression: insights from proteomics, single-cell transcriptomics and genomics by Chaonan Wang, Yuyao Feng, Xiaoyan Liu, Haidan Sun, Zhengguang Guo, Jiang Shao, Kang Li, Junye Chen, Keqiang Shu, Deqiang Kong, Jiaxian Wang, Yiran Li, Xiangling Lei, Chen Li, Bao Liu, Wei Sun, Zhichao Lai

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Transcriptomic signatures of neonatal acute respiratory distress syndrome in a prospective cohort of respiratory distress by Chan Liu, Qing Ai, Jingli Yang, Ying Fan, Wen Jia, Leyu Si, Yuting Yao, Feifan Chen, Shiyue Liu, Yu He, Yuan Shi

“…This study characterized whole blood transcriptomic profiles of NARDS in a pilot cohort of 48 neonates with respiratory distress, demonstrating a significant GA-dependent modulation of gene expression. …”
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Transcriptome and hormonal analyses reveal an important role of auxin and cytokinin in regulating rice ratooning ability by Can Hu, Chenfan Zheng, Bo Liu, Like Sun, Jiaxi Yin, Yuanyuan Tan, Pedro García-Caparros, Qingyao Shu, Meng Jiang

“…In the present study, the RA trait was evaluated in 23 rice varieties cultivated across three different locations in Hainan Province, showing substantial phenotypic variation. …”
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Molecular Mechanism of <i>Cuscuta</i> Haustorium Specialization Inferences from Transcriptome and Metabolome Analysis by Xingpan Meng, Ning Lv, Xinglin Wang, Qihang Zhou, Xu Zhang, Ximin Zhang, Zhengdong Zhang, Lunxian Liu, Tie Shen

“…Var Williams</i>) through comprehensive transcriptomic and metabolomic analyses. Results: The results demonstrated significant differences in the gene expression and metabolic features between the haustorium and the distal stem segments. …”
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Integrative Analysis of Transcriptome and Metabolome to Illuminate the Protective Effects of Didymin against Acute Hepatic Injury by Lijun Pang, Yuhua Xiong, Zhongwen Feng, Cuiyu Li, Bin Fang, Quanfang Huang, Xing Lin

“…Meanwhile, the metabolome analysis revealed 67 differently expressed metabolites (DEMs) between the didymin and model groups that were mainly clustered into the glycerophospholipid metabolism, which was consistent with the transcriptome study. …”
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Whole transcriptome analysis of breast tumors during neoadjuvant chemotherapy: association with response to preoperative chemotherapy by M. K. Ibragimova, M. M. Tsyganov, N. V. Litviakov

“…We performed whole-transcriptome analysis of paired biopsy and surgical specimens using the Clariom™ S Assay, human (Affymetrix, USA).Results. …”
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Pituitary Transcriptome Analysis of Genes and Pathways Related to Traits at the First Egg in Kangle Yellow Chicken by Jinge MA, Lan LAN, Zige LIU, Jiguo XU

“…【Objective】This study focus on Kangle yellow chickens, using transcriptome sequencing technology to deeply analyze the differences in pituitary transcriptome expression profiles of laying and pre-laying individuals at 154 days of age, aiming to screen the genes and signal pathways closely related to laying traits in the pituitary gland.…”
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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

“…Fatty acid (FA) analysis identified 15 significant FAs in the LWLDP, with docosahexaenoic acid (DHA) in the SBP, while amino acid (AA) analysis revealed no breed-based differences. Transcriptome analysis identified 134 upregulated and 362 downregulated genes in the SBP. …”
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Untargeted metabolomics and transcriptomics joint analysis of the effects of polystyrene nanoplastics on lipid metabolism in the mouse liver by Lijuan Chen, Guoyuan Sui, Jin Wu, Ning Li, Zhe Zhang, Ying Du, Meijun Lü, Xiaorui Yan, Guowei Pan, Lianqun Jia

“…Additionally, transcriptomics reveals that differentially expressed genes (DEGs) triggered by NPs exposure are predominantly involved in metabolic routes including lipid metabolism and cytochrome P450 (CYP). …”
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Transcriptomic Analysis of Skin Tissue Reveals Molecular Mechanisms of Thermal Adaptation in Cold-Exposed Lambs by Mengyu Feng, Kaixi Ji, Yutao Li, Pâmela Almeida Alexandre, Dan Jiao, Yanping Liang, Xia Du, Xindong Cheng, Huitong Zhou, Jon G. H. Hickford, Guo Yang

“…Skin tissues were analyzed with transcriptome sequencing, and selected wool and physiological traits were assessed. …”
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DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads by Kailu Song, Yumin Zheng, Bowen Zhao, David H. Eidelman, Jian Tang, Jun Ding

“…DOLPHIN not only demonstrates superior performance in cell clustering, biomarker discovery, and alternative splicing detection but also provides a distinct capability to detect subtle transcriptomic differences at the exon level that are often masked in gene-level analyses. …”
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Transcriptome sequencing reveals the evolutionary histories and gene expression evolution in two related Pagurus species. by Zakea Sultana, Isaac Adeyemi Babarinde, Masafumi Nozawa, Kazuho Ikeo, Akira Asakura, Tomoyuki Nakano

“…To investigate the molecular and gene expression evolution that have followed the divergence of these two species, we performed transcriptome sequencing and de novo transcriptome assembly using cephalothorax (head) and pereopod (leg) of the two species. …”
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Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis by Pradeep K. Yadalam, Prabhu Manickam Natarajan, Carlos M. Ardila

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Identification of Potential Biomarkers of Septic Shock Based on Pathway and Transcriptome Analyses of Immune-Related Genes by Jie Wang, Jie Cai, Linlin Yue, Xixi Zhou, Chunlin Hu, Hongquan Zhu

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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. …”
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Evaluating the Anticancer Potential of Ornithogalum saundersiae Saponins on Hepatocellular Carcinoma: A Transcriptome Sequencing Method by Bo XU, Ting JIANG, Wangde JIN, Xinglin JIN

“…A total of 1381 genes showed significant differences in expression as a result of transcriptome sequencing, with a majority being involved in the TNF signaling pathway. …”
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Single-cell transcriptomics and tissue metabolomics uncover mechanisms underlying wooden breast disease in broilers by Di Zhao, Zehe Song, Li Shen, Tian Xia, Qingyuan Ouyang, Haihan Zhang, Xi He, Kelang Kang

“…We have performed a comprehensive transcriptomic and metabolomic atlas of chicken WB muscle. …”
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A transcriptomic and proteomic analysis and comparison of human brain tissue from patients with and without epilepsy by Taiyang Zhu, Yan Zhou, Lei Zhang, Lingwen Kong, Hai Tang, Qihua Xiao, Xiaoyu Sun, Fanyu Shen, Hui Zhou, Wanyan Ni, Sha Liu, Huimin Gao, Guoliang Jin, Xiao Jia, Fang Hua

“…Tubulin polymerization promoting protein family member-3 (TPPP3), proprotein convertase subtilisin/kexin type-1 (PCSK1), and dihydropyrimidinase-like 3 (DPYSL3) were significantly altered in the epilepsy patients, and their expression trends were confirmed by the RT-qPCR, WB, and IHC staining results. By integrating transcriptomic and proteomic analyses, we identified genes and proteins expressed differently in epileptic and non-epileptic patients and their associated biological processes. …”
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Transcriptomic profiling to unravel the underlying causes of early gonadal development of hilsa (Tenualosa ilisha) in Bangladesh by A. K. Shakur Ahammad, Md. Baktiar Abid, Ilias Ahmed, Mariom, Mohd Golam Quader Khan, Mohammad Mahfujul Haque, Li Lian Wong, Mohammad Ashraful Alam, Md. Abul Bashar

“…A total of 908 DEGs were detected, of which 453 were up-regulated and 455 were down-regulated. Transcriptome analysis revealed significant differences in Gene Ontology terms such as extracellular region (GO:0005576), innate immune response (GO:0045087), and protein ubiquitination (GO:0016567), peptide antigen binding (GO:0042605), KEGG pathways including MAPK signaling pathway (ko04010), endocytosis (ko04144), and spliceosome (ko03040), as well as COG terms like signal transduction, between the ovary of large and small hilsa shad. …”
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Soil-Mulching Treatment Enhances the Content of Stilbene in Grape Berries: A Transcriptomic and Metabolomic Analysis by Bo Wang, Weimin Wu, Zhuangwei Wang, Zhenxiao Chen, Xicheng Wang

“…The results of the cluster analysis and orthogonal projection to latent structures discriminant analysis of the metabolites showed a difference between the mulching and control groups, as did the principal component analysis results for the transcriptome. …”
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