Cell type differences in human cytomegalovirus transcription and epigenetic regulation with insights into major immediate-early enhancer-promoter control. by Qiaolin Hu, Ming Li, Mrutyunjaya Parida, Benjamin M Spector, Juan F Santana, Arya Zandvakili, David H Price, Jeffery L Meier

“…Cell type differences in the human cytomegalovirus (HCMV) transcriptome may arise from variations in transcription or post-transcription regulation. …”
Get full text

Molecular mechanisms of cryoablation-mediated lung cancer suppression unveiled by non-coding RNA regulatory network profiling by Xiaofan Wang, Mohan Zhang, Dianna Liu, Shicheng Lin, Yuxin Zhang, Quanwang Li

“…Abstract While cryoablation demonstrates therapeutic potential for lung adenocarcinoma, the precise molecular mechanisms underlying its antitumor effects require further elucidation. …”
Get full text

Alternative splicing dynamics during gastrulation in mouse embryo by Wei Wang, Yu Zhang, Yuanyuan Zhai, Wuritu Yang, Yongqiang Xing

“…Subsequently, the dynamic expression of splicing factors (SFs) during gastrulation was characterized, while the expression patterns and functions of germ layer-specific SFs were identified. …”
Get full text

An insulin-sensitive Drosophila insulin-like receptor mutant remodels methionine metabolism to extend lifespan. by Marc Tatar, Wenjing Zheng, Shweta Yadav, Rochele Yamamoto, Noelle Curtis-Joseph, Shengxi Li, Lin Wang, Andrey A Parkhitko

“…Type I and II mutants overlap in many pathways but also produce distinct transcriptomic profiles that include differences in innate immune and reproductive functions. …”
Get full text

In-depth and high-throughput spatial proteomics for whole-tissue slice profiling by deep learning-facilitated sparse sampling strategy by Ritian Qin, Jiacheng Ma, Fuchu He, Weijie Qin

“…Therefore, spatially resolved gene expression profiling is crucial for determining the function and phenotypes of these cells. While genome mutations and transcriptome alterations act as drivers of diseases, the proteins that they encode regulate essentially all biological functions and constitute the majority of biomarkers and drug targets for disease diagnostics and treatment. …”
Get full text

The transcription factors Snail and Slug activate the transforming growth factor-beta signaling pathway in breast cancer. by Archana Dhasarathy, Dhiral Phadke, Deepak Mav, Ruchir R Shah, Paul A Wade

“…Of particular interest, genes involved in the TGF-beta signaling pathway are upregulated, while genes responsible for a differentiated morphology are downregulated following Snail or Slug expression. …”
Get full text

FGF7 secreted from dermal papillae cell regulates the proliferation and differentiation of hair follicle stem cell by Niu Wang, Weidong Zhang, Zhenyu Zhong, Xiongbo Zhou, Xinran Shi, Xin Wang

“…FGF7 functions as a paracrine protein regulating epithelial proliferation, differentiation and migration. The single-cell transcriptome profiling and immunofluorescence analysis demonstrated that FGF7 localizes at DPC, while FGF7 receptor (FGFR2) expresses in both DPC and HFSC. …”
Get full text

PRDX1 knockdown promotes erastin-induced ferroptosis and impedes diffuse large B-cell lymphoma development by inhibiting the MAPK/ERK pathway by Chuanming Lin, Shuiling Xie, Menger Wang, Jianzhen Shen

“…A xenograft tumor model was constructed to verify the roles of PRDX1 in vivo. Transcriptome sequencing was conducted to identify PRDX1-mediated signaling pathways. …”
Get full text

Global changes in gene expression of Barrett's esophagus compared to normal squamous esophagus and gastric cardia tissues. by Paula L Hyland, Nan Hu, Melissa Rotunno, Hua Su, Chaoyu Wang, Lemin Wang, Ruth M Pfeiffer, Barbara Gherman, Carol Giffen, Cathy Dykes, Sanford M Dawsey, Christian C Abnet, Kathryn M Johnson, Ruben D Acosta, Patrick E Young, Brooks D Cash, Philip R Taylor

“…<h4>Background</h4>Barrett's esophagus (BE) is a metaplastic precursor lesion of esophageal adenocarcinoma (EA), the most rapidly increasing cancer in western societies. While the prevalence of BE is increasing, the vast majority of EA occurs in patients with undiagnosed BE. …”
Get full text

Downregulation of Notch Signaling‐Stimulated Genes in Neurovascular Unit Alterations Induced by Chronic Cerebral Hypoperfusion by Dewen Ru, Zengyu Zhang, Meng Liu, Xuhui Fan, Yuqi Wang, Yufeng Yan, Ersong Wang

“…Upregulated differentially expressed genes (DEGs) were enriched in microglia/macrophages, while downregulated DEGs were prominent in endothelial cells and pericytes. …”
Get full text

Comparing Xenium 5K and Visium HD data from identical tissue slide at a pathological perspective by Mengping Long, Taobo Hu, Weixin Wang, Junshun Gao, Nan Wang, Mats Nilsson

“…While sequencing-based Visium HD features a refined bin size of 2 µm and transcriptome wide coverage, Xenium in-situ is a targeted imaging-based detection technology with sub-micron resolution. …”
Get full text

Comparative Analysis of Proximal Tubule Cell Sources for In Vitro Studies of Renal Proximal Tubule Toxicity by Courtney Sakolish, Han-Hsuan D. Tsai, Hsing-Chieh Lin, Piyush Bajaj, Remi Villenave, Stephen S. Ferguson, Jason P. Stanko, Richard A. Becker, Philip Hewitt, Weihsueh A. Chiu, Ivan Rusyn

“…The CellTiterGlo^® assay was used to measure cell viability, and transcriptome data from unexposed cells was analyzed using the TempO-seq^® S1500+ platform. …”
Get full text

γ-Aminobutyric Acid Alleviates Salinity-Induced Impairments in Rice Plants by Improving Photosynthesis and Upregulating Osmoprotectants and Antioxidants by Jiaxin Feng, Tianyang Zhou, Yibiao Gu, Chenchen Shu, Kuanyu Zhu, Weiyang Zhang, Hao Zhang, Lijun Liu, Zhiqin Wang, Junfei Gu, Jianchang Yang

“…These helped maintain photosynthesis under saline conditions while reducing water consumption.…”
Get full text

Effects of Dietary β-Carotene on the Gonadal Color, Pigmentation, and Regulation Mechanisms in Sea Urchin Strongylocentrotus Intermedius by Weixiao Di, Yinuo Zhang, Huinan Zuo, Haijing Liu, Lina Wang, Jun Ding, Yaqing Chang, Rantao Zuo

“…Several differential genes, enriched in the pathways of steroid biosynthesis, oxidative phosphorylation, and ubiquitination, were screened based on transcriptome analysis. Real-time PCR further demonstrated that β-carotene significantly upregulated the expression of <i>cholesterol 25-hydroxylase</i> (<i>CH25H</i>), <i>NADH dehydrogenase subunit 1</i> (<i>ND1</i>), <i>NADH dehydrogenase subunit 2</i> (<i>ND2</i>), and <i>NADH dehydrogenase subunit 4</i> (<i>ND4</i>) while it downregulated the expression of <i>24-dehydrocholesterol reductase</i> (<i>DHCR24</i>). …”
Get full text

Instantaneous dose rate as a crucial factor in reducing mortality and normal tissue toxicities in murine total-body irradiation: a comparative study of dose rate combinations by Hongyu Zhu, Shihua Liu, Jiaqi Qiu, Ankang Hu, Wanyi Zhou, Jian Wang, Weihang Gu, Yinuo Zhu, Hao Zha, Rong Xiang, Junli Li, Rui Qiu, Chong Zhao, Peng Huang, Xiaowu Deng

“…Abstract Purpose The ultra-high dose rate (UHDR) radiation shows promise in eradicating tumors while reducing normal tissue toxicities. However, the biological outcomes of UHDR are influenced by various factors, particularly the mean dose rate and instantaneous dose rate. …”
Get full text

Immunomodulatory gene networks predict treatment response and survival to de-escalated, anthracycline-free neoadjuvant chemotherapy in triple-negative breast cancer in the WSG-ADAP... by Darren Korbie, Clare Stirzaker, Oleg Gluz, Christine zu Eulenburg, Ulrike Nitz, Matthias Christgen, Sherko Kuemmel, Eva-Maria Grischke, Helmut Forstbauer, Michael Braun, Mathias Warm, John Hackmann, Christoph Uleer, Bahriye Aktas, Claudia Schumacher, Rachel Wuerstlein, Enrico Pelz, Hans Heinrich Kreipe, Susan J. Clark, Matt Trau, Monika Graeser, Nadia Harbeck

“…Immune recruitment and viral defense gene networks were strongly associated with pCR, while metabolic pathways were associated with survival. …”
Get full text

Comparative analysis of genotype imputation strategies for SNPs calling from RNA-seq by Kaixuan Guo, Zhanming Zhong, Haonan Zeng, Changliang Zhang, Teddy Tinashe Chitotombe, Jinyan Teng, Yahui Gao, Zhe Zhang

“…Abstract Background RNA sequencing (RNA-seq) is a powerful tool for transcriptome profiling, enabling integrative studies of expression quantitative trait loci (eQTL). …”
Get full text

Entrectinib can induce nerve cell damage by inhibiting PI3K-AKT and TGF-β signaling pathways by Qingshan Tang, Jiachen Dong, Feng Zhang, Dan Zhao, Qi Yang, Jiayu Wen, Yuhao Sun, Jifu Wei, Zhixian Liu

“…Cell apoptosis was measured by flow cytometry. Next, transcriptome sequencing technology was performed to identify differentially expressed genes (DEGs). …”
Get full text

Discovering biomarkers associated with infiltration of CD8+ T cells and tumor-associated fibrosis in colon adenocarcinoma using single-cell RNA sequencing and gene co-expression ne... by Jinning Zhang, Jinning Zhang, Ziquan Sun, Ziquan Sun, Guodong Li, Guodong Li, Lixian Ding, Zitong Wang, Ming Liu, Ming Liu

“…Therefore, it is imperative to identify biomarkers with prognostic value and elucidate the precise role of CD8+ T cells and tumor-associated fibrosis.MethodsWe performed a single-cell transcriptome analysis of COAD samples from the GEO database. …”
Get full text

ELABELA promotes the migration and homing of bone marrow mesenchymal stem cells to myocardial injury sites through the ERK1/2/miR-299a-5p/Exo70 pathway by Jing-Yu Hou, Hao Wu, Shuang-Mei Li, Xiao-Jing Li, Shu-Jun Yang, Xu-Xiang Chen, Chang-Qing Zhou, Hui-Bao Long, Hai-Dong Wu, Jia-Ying Fu, Ya-Jie Guo, Tong Wang

“…Cardiac repair was evaluated through fluorescence imaging, echocardiography, and histological analysis. Transcriptome sequencing and bioinformatics analysis were employed to identify and validate the mechanisms by which ELA promoted the migration of BMSCs. …”
Get full text