Bioinformatic Analysis of Apoptosis-Related Genes in Preeclampsia Using Public Transcriptomic and Single-Cell RNA Sequencing Datasets by Liu L, Li X, Yang H, Xu F, Dong X

“…Endothelial cell communication with other cell types decreased, while the interaction between common myeloid progenitors (CMP) and villous cytotrophoblasts (VCT) enhanced. …”
Get full text

Single-cell transcriptome and multi-omics integration reveal ferroptosis-driven immune microenvironment remodeling in knee osteoarthritis by Yushun Wu, Jing Liu, Wenying Yu, Xiaoding Wang, Jian Li, Weiquan Zeng

“…BackgroundKnee osteoarthritis (KOA) is a chronic inflammatory joint disorder marked by cartilage degradation and immune microenvironment dysregulation. While transcriptomic studies have identified key pathways in KOA, the interplay between ferroptosis (an iron-dependent cell death mechanism) and immune dysfunction at single-cell resolution remains unexplored. …”
Get full text

Combined Analysis of Transcriptome and Mendelian Randomization Reveals AKT1 and PPARG as Biomarkers Related to Glucose Metabolism in Sepsis by Ma J, Li W, Ma Q, Ding L, Wang Z, Wang R, Huang Y, Ma G, Gao J

“…AKT1 may inhibit sepsis development, while PPARG may promote it. These findings provide valuable insights for sepsis diagnosis and therapeutic drug development.Keywords: sepsis, glucose metabolism, transcriptomics, Mendelian randomization, biomarkers…”
Get full text

Desert-adapted tomato Solanum pennellii exhibit unique regulatory elements and stress-ready transcriptome patterns to drought. by J Sebastián Contreras-Riquelme, Miguel Contreras, Tomas C Moyano, Rachid Sjoberg, José Jimenez-Gomez, José M Alvarez

“…Approximately 43% of the orthologous genes exhibited species-specific expression patterns, while nearly 20% were classified as stress-ready. …”
Get full text

Effects of chlorogenic acid on growth performance, immunity, antioxidant capacity, intestinal microbiota, and liver transcriptome in Mauremys mutica by Hongyao Zhang, Jingu Shi, Zike Yan, Mingzuo Gao, Kaijie Lin, Yutian Zhan, Yuhan Li, Jingzhen Liang, Shuyu Han

“…Serum levels of alkaline phosphatase (AKP), acid phosphatase (ACP), complement C3, and complement C4 were elevated, while superoxide dismutase (SOD) and catalase (CAT) activities increased. …”
Get full text

Integrative analysis of metabolomics and transcriptomics reveals alterations in egg quality and hepatic lipid metabolism in hens supplemented with curcumin by Cunzhi Zou, Haiyu Jiang, Xuanfu Wu, Jiang Gao, Wenqiang Ma

“…The control group was fed a basal diet, while the experimental groups received diets supplemented with either 50 or 100 mg/kg of curcumin for 42 days. …”
Get full text

Integrative Transcriptome and Metabolome Analysis Identifies Potential Pathways Associated with Cadmium Tolerance in Two Maize Inbred Lines by Pingxi Wang, Min Li, Xingye Ma, Bin Zhao, Xining Jin, Huaisheng Zhang, Shilin Chen, Xiangyuan Wu, Xiaoxiang Zhang

“…Physiological assessments revealed that C7_2 maintained relatively stable antioxidant enzyme activity, while Z58 demonstrated more rapid alterations in the antioxidant system under Cd stress. …”
Get full text

Integration of Transcriptomics and Metabolomics Reveals Mechanisms of High-Temperature Stress Tolerance in the Hepatopancreas of <i>Penaeus monodon</i> by Li Liu, Peng Zhao, Lishi Yang, Yundong Li, Zhong Huang, Qibin Yang, Yukai Yang, Jianzhi Shi, Yibiao Chen, Jianhua Huang

“…The heat-sensitive shrimps (S group) were collected in the first 24 h, while those that survived beyond 120 h were collected as the heat-tolerant group (T group). …”
Get full text

Integrated transcriptomic and metabolomic analysis reveals the effects of EMMPRIN on nucleotide metabolism and 1C metabolism in AS mouse BMDMs by Yun Zhang, Diyuan Zhang, Zulong Xie, Tianli Xia, Lili Zou, Tao Wang, Li Zhong, Zhuo Zeng, Lingying Wang, Guozhu Chen, Xing Liang

“…Metabolomic results identified increased levels of glycine, serine, betaine and S-adenosyl-L-methionine (SAM) to S-adenosyl-L-homocysteine (SAH) ratio and decreased levels of dimethylglycine (DMG) and SAH in 1C metabolism, accompanied by the accumulation of nucleotides, nucleosides, and bases in nucleotide metabolism. Transcriptomics results shown that Dnmt, Mthfd2 and Dhfr were downregulated, while Mthfr were upregulated in 1C metabolism. …”
Get full text

Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis by Nathan Nakatsuka, Drew Adler, Longda Jiang, Austin Hartman, Evan Cheng, Eric Klann, Rahul Satija

Get full text

Single-cell transcriptomics unveils multifaceted immune heterogeneity in early-onset versus late-onset cervical cancer by Qian Chen, Dongfeng Deng, Hong Zhu, Shan Li

“…CD4 + and CD8 + T cells in LOCC demonstrated a heightened activation state, while NK cells exhibited diminished cytotoxicity. …”
Get full text

Comparative Transcriptome Analysis of Gene Responses of Salt-Tolerant and Salt-Sensitive Watermelon Cultivars’ Roots to Salt Stress by Peng Liu, Chao Gao, Shuai Li, Xudong Wang, Yumei Dong, Chongqi Wang, Zigao Jiao, Jianlei Sun

“…The provided physiological data demonstrate that T23 exhibits superior antioxidant and osmoregulatory abilities relative to B2. The transcriptome analysis identified differentially expressed genes (DEGs) between the two cultivars under salt stress, with T23 showing the highest number of DEGs at 6 h, while B2 exhibited a significant increase in DEGs at 168 h. …”
Get full text

Comparative transcriptome analysis reveals the potential mechanism of seed germination promoted by trametenolic acid in Gastrodia elata Blume by Jie Liu, Wangyang Ye, Danyang Wang, Hongqi Zhang, Junzhi Wang, Dongwei Li

“…Six genes were confirmed using qRT-PCR: Down-regulated genes in the lignin biosynthesis pathway include MYB4 and 4CL, while GA20ox1 in the gibberellin biosynthesis pathway was also down-regulated. …”
Get full text

Germline structural variations involving the pediatric brain tumor transcriptome include disease-relevant and ancestry-related genes by Fengju Chen, Yiqun Zhang, Luis F. Paulin, Fritz J. Sedlazeck, Chad J. Creighton

Get full text

Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation. by Archana Prabahar, Connie S Chamberlain, Ray Vanderby, William L Murphy, William Dangelo, Kulkarni Mangesh, Bryan Brown, Barsanjit Mazumder, Stephen Badylak, Peng Jiang

“…In the mouse distal terminal phalanx (P3), it remains mystery why amputation at less than 33% of the digit results in regeneration, while amputation exceeding 67% leads to non-regeneration. …”
Get full text

Combined Effects of Marine Heatwaves and Light Intensity on the Physiological, Transcriptomic, and Metabolomic Profiles of <i>Undaria pinnatifida</i> by Hanmo Song, Yan Liu, Qingli Gong, Xu Gao

“…Following severe MHW exposure, the partial recovery of some physiological traits was observed, while photosynthetic capacity, membrane integrity, and energy metabolism remained impaired, and oxidative damage was not fully resolved. …”
Get full text

Unraveling ScAPD1-mediated resistance mechanism to Verticillium dahliae through integrated host-pathogen transcriptomics by Qilin Yang, Ruirui Yang, Huan Zhang, Fangliu Yin, Leyi Wang, Daoyuan Zhang, Xiaoshuang Li

“…Phenotypic analysis confirmed enhanced resistance in transgenic A. thaliana overexpressing ScAPD1 (SC lines), characterized by attenuated disease symptoms and significantly reduced fungal biomass. Transcriptomic analysis revealed a striking divergence in host response: while V. dahliae infection severely suppressed photosynthesis-related pathways in wild-type (WT) plants, SC lines maintained their photosynthetic capacity; this preservation of primary metabolism indicates a key component of ScAPD1-mediated resistance. …”
Get full text

SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data by Diane Zhang, Åsa Segerstolpe, Michal Slyper, Julia Waldman, Evan Murray, Robert Strasser, Jan Watter, Ofir Cohen, Orr Ashenberg, Daniel Abravanel, Judit Jané-Valbuena, Simon Mages, Ana Lako, Karla Helvie, Orit Rozenblatt-Rosen, Scott Rodig, Fei Chen, Nikhil Wagle, Aviv Regev, Johanna Klughammer

“…SlideCNA uses expression-aware spatial binning to overcome sparsity limitations while maintaining spatial signal to recover CNA patterns. …”
Get full text

Selection and validation of reference genes for qRT-PCR normalization in dayflower (Commelina communis) based on the transcriptome profiling by Yuejiao Yang, Gaohui Cao, Lulu Tang

Get full text

Transcriptomic Profiling Unravels the Disruption of Photosynthesis Apparatuses and Induction of Immune Responses by a Bipartite Begomovirus in Tomato Plants by Wen-Ze He, Ting Rong, Xun-Yue Liu, Qiong Rao

“…We then profiled the tomato transcriptomic changes in response to TYLCTHV infection. …”
Get full text