Identifying common pathways for doxorubicin and carfilzomib-induced cardiotoxicities: transcriptomic and epigenetic profiling by Conagh Kelly, Dylan J. Kiltschewskij, Angeline J.W. Leong, Tatt Jhong Haw, Amanda J. Croft, Lohis Balachandran, Dongqing Chen, Danielle R. Bond, Heather J. Lee, Murray J. Cairns, Aaron L. Sverdlov, Doan T. M. Ngo

Get full text

Transcriptome Analysis Reveals the Requirement of the TGFβ Pathway in Ascidian Tail Regression by Wenjie Shi, Penghui Liu, Dongyu Yang, Yuan Zhuang, Boyan Lin, Bo Dong

“…We further investigated the downstream gene network of the TGFβ signaling pathway through comparative transcriptome data analysis on the TGFβ pathway inhibition samples. …”
Get full text

Transcriptomic, and metabolic profiling reveals adaptive mechanisms of Auricularia heimuer to temperature stress by Chenhong Nie, Shiyan Wei, Shengjin Wu, Liangliang Qi, Jing Feng, Xiaoguo Wang

“…Here, we performed a comprehensive morphologic, transcriptomic, and metabolic analysis of A. heimuer mycelium exposed to different temperatures over a long period of time. …”
Get full text

Combined Genomic and Transcriptomic Screening of Candidate Genes for Asymmetric Oviduct Development in Hens by Ruijie Li, Xiang Song, Xiao Lin, Mingli Deng, Yin Liu, Tuoyu Geng, Daoqing Gong, Minmeng Zhao, Long Liu

Get full text

Transcriptomic responses to transportation stress in the juvenile Chinese sea bass (Lateolabrax maculatus) by Yue Su, Sarinpan Kokau, Xiao-Ning Zhang, Yun-Wei Dong

“…In the present study, the transcriptomic profiles in the brain and liver of Chinese sea bass (Lateolabrax maculatus) were characterized after transportation stress at two different densities (low-density: 20 kg/m3 and high-density: 40 kg/m3). …”
Get full text

Whole-Transcriptome Analysis Reveals the Regulatory Network of Immune Response in Dapulian Pig by Tao Wang, Zhe Tian, Mubin Yu, Shuer Zhang, Min Zhang, Xiangwei Zhai, Wei Shen, Junjie Wang

“…Generally, the immune response is an important part of anti-disease capability; however, the related mechanism in pigs is largely puzzling. Here, the public transcriptome data of peripheral blood mononuclear cells (PBMCs) from Dapulian (Chinese local breed) and Landrace (Commercial breed) pigs after stimulation with polyinosinic-polycytidylic acid (poly I:C, a conventional reagent used for simulation of the viral infection) were reanalyzed, and the immune response mechanism in different pig breeds was investigated from a transcriptomic perspective. …”
Get full text

Integration of single cell and bulk transcriptomes identifies T cell stress subtypes in LUAD by Shengping Min, Linfeng Pan, Xinyu Zhang, Huili Chen, Lixuan Qiu, Xinyu Wang, Yiluo Xie, Kai Zhang, Qiang Zhang, Chaoqun Lian, Jing Zhang

“…Methods The categorization and validation of cluster types for Tstr signature genes were systematically carried out using transcriptomic data sourced from the TCGA and GEO databases. …”
Get full text

Histological, physiological and transcriptomic analysis in hepatopancreas of Procambarus clarkii under heat stress by Yongfeng Zou, Panhui Cao, Zhiming Bao, Yu Xu, Zhiqiang Xu, Hui Guo

“…In the present study, a comprehensive analysis in hepatopancreas from Procambarus clarkii was conducted to examine the histology, physiological changes, and transcriptome alterations after exposed at 32 and 37 ℃ for 24 and 72 h, respectively, with 26 ℃ as the control group. …”
Get full text

Integration of metabolomics and transcriptomics to reveal anti-immunosuppression mechanism of Lycium barbarum polysaccharide by Jiandong Wang, Xue Zhang, Yi Wu, Yi Wu, Qianfei Wei, Lingshan Yan, Youli Yu, Yanan Guo, Zhengqin Yu, Pan Wang, Xiaonan Yang

“…The integrated examination of transcriptomic and metabolomic data revealed that the glycerophospholipid metabolic pathway stands out as the most significant among all metabolic pathways. …”
Get full text

Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Lagerstroemia indica petals by Xian Xie, Tiantian Cheng, Yu Yan, Cuicui Zhu, Ming Zhang, Zhongkui Sun, Ting Wang

“…We used LC-MS/MS and RNA-seq to uncover the genetic basis of flower colour variation with the help of the metabolome and transcriptome of three varieties with different colored petal, ‘Huahai’, ‘Zhuimeng’, ‘Zixian’. …”
Get full text

Transcriptomic time course of skeletal muscle disuse and rehabilitation in middle‐aged adults by Zachary D. Von Ruff, Sean P. Kilroe, Erik D. Marchant, Emily J. Arentson‐Lantz, Steven Widen, Jill Thompson, Alejandro Villasante‐Tezanos, Elena Volpi, Doug Paddon‐Jones, Blake B. Rasmussen

“…This study aimed to characterize phenotypic and transcriptomic skeletal muscle changes in middle‐aged individuals during disuse and rehabilitation. …”
Get full text

Multi-tissue transcriptomic characterization of endogenous retrovirus-derived transcripts in Capra hircus by Ming-Di Li, Ming-Di Li, Hu-Rong Li, Shao-Hui Ye

“…They showed strong co-expression with their proximal gene OAS1 and TMPRSS2, indicating the impact of activated proximal gene expression on nearby ERVs.ConclusionWe generated ERV transcriptomes across goat tissues, and identified ERVs activated in response to different physiological and pathological conditions.…”
Get full text

Transcriptome Analysis Provides Insights into the Safe Overwintering of Local Peach Flower Buds by Ruxuan Niu, Yongjuan Cheng, Falin Wang, Yiwen Zhang, Chenbing Wang

“…The antioxidant enzyme activity, levels of malondialdehyde (MDA), proline (Pro), and hydrogen peroxide content (H₂O₂) were determined in peach buds at different dormancy periods. Transcriptome sequencing was performed at three dormancy stages: the dormancy entry stage (FD), deep dormancy release stage (MD), and dormancy release stage (RD). …”
Get full text

De novo transcriptome assembly and annotation of the semi-wild Gayal (Bos frontalis) by Zhendong Gao, Bo Wang, Ying Lu, Yuqing Chong, Mengfei Li, Jieyun Hong, Jiao Wu, Dongmei Xi, Weidong Deng

“…In this study, an integrated PacBio Iso-seq and RNA-seq analysis was conducted on samples from 10 different organs and tissues of the Gayal, with each being sequenced in triplicate. …”
Get full text

Integration of metabolomics and transcriptomics analyses reveals the effects of nano-selenium on pak choi by Yanyan Wang, Peiheng Sun, Mingying Nie, Jianyun Zhan, Liu Huang, Junda Wu, Jie Zhang, Xiaowu He, Na Li, Longsong Hu, Shiyu Liu, Chengfu Yuan, Changming Zhou, Guangjie Chen, Jialong Huang, Xiaofei Li

“…Therefore, this study aims to investigate the impact of nano-selenium on pak choi through an integrated analysis of transcriptome and metabolome. Specifically, we examined the effects of different concentrations of nano-selenium (0, 5, 10 and 20 mg L−1) on the growth and nutritional quality of Suzhouqing. …”
Get full text

Transcriptome-scale analysis of functional alternative back-splicing events in colorectal cancer by Qianqian Ning, Qian Jin, Lei Zhao, Yudi Wang, Jie Wang, Lili Yang, Ye Han, Qiaoming Zhi, Junnian Zheng, Feifei Chen, Dong Dong

“…The result showed that overexpression of circXPO1-2 inhibited CRC cell proliferation, migration, and invasion in vitro and in vivo, whereas circXPO1-1 is not, indicating that the circularization isoforms of XPO1 gene have different functions in CRC. Conclusions In conclusion, our work provides the landscape of ABS events in CRC transcriptome and the close association of ABS circRNAs with tumorigenesis offers a new set of targets with potential clinical benefit.…”
Get full text

Seasonal transcriptomic shifts reveal metabolic flexibility of chemosynthetic symbionts in an upwelling region by Isidora Morel-Letelier, Benedict Yuen, Luis H. Orellana, A. Carlotta Kück, Yolanda E. Camacho-García, Minor Lara, Matthieu Leray, Laetitia G. E. Wilkins

“…We observed a concerted shift in the transcriptomic profiles of both symbiont clades before and during upwelling, suggesting changes in energy source use. …”
Get full text

Effects of supplementary light treatment on saffron: integrated physiological, metabolomic, and transcriptome analyses by Li Li, Yujie Zhou, Jingting Wang, Xiwu Qi, Hailing Fang, Yang Bai, Zequn Chen, Xu Yu, Dongmei Liu, Qun Liu, Chengyuan Liang

“…We investigated saffron growth and flowering using non-target metabolomic and transcriptome analyses to determine the flux and accumulation of metabolites from the stigma under different light treatments. …”
Get full text

Comparative transcriptomics reveal stage-dependent parasitic adaptations in the myxozoan Sphaerospora molnari by Monika M. Wiśniewska, Jiří Kyslík, Gema Alama-Bermejo, Alena Lövy, Martin Kolísko, Astrid S. Holzer, Anush Kosakyan

“…We hypothesize that these parasite life-stages differ in regards to their host exploitation, pathogenicity, and host immune evasion strategies and mechanisms. …”
Get full text

Integrated transcriptomic and metabolomic analysis reveals drivers of protein and oil variation in cottonseed by Chaoze Zhou, Yiwen Huang, Dayu Zhou, Yuzhen Wu, Shouyang Fu, Longyu Huang, Jun Peng, Meng Kuang

“…The protein and oil content in cottonseed, known for their high quality, exhibits substantial variation across different cotton varieties. This study explored the regulatory mechanisms behind these differences by analyzing protein and oil accumulation patterns, transcriptomics, and metabolomics in two cotton varieties during seed development. …”
Get full text