Integrative single-cell and cell-free plasma RNA transcriptomics identifies biomarkers for early non-invasive AD screening by Li Wu, Li Wu, Renxin Zhang, Renxin Zhang, Yichao Wang, Yichao Wang, Shaoxing Dai, Shaoxing Dai, Naixue Yang, Naixue Yang

“…A systematic comparative analysis of cfRNA and brain scRNA-seq datasets was conducted to identify dysregulated genes linked to AD pathology. …”
Get full text

Comparative transcriptomics of two petal variants reveals key functional genes underlying petal shape development in lotus (Nelumbo) by Jiaxin He, Jiaxin He, Yini Ma, Qingqing Liu, Rui Zhang, Guohong Huang, Dasheng Zhang, Fengluan Liu, Caixia Yang

Get full text

Integrated hepatic transcriptomics and metabolomics identify Pck1 as a key factor in the broad dysregulation induced by vehicle pollutants by Gajalakshmi Ramanathan, Yuqi Zhao, Rajat Gupta, Siri Langmo, May Bhetraratana, Fen Yin, Will Driscoll, Jerry Ricks, Allen Louie, James A. Stewart, Timothy R. Gould, Timothy V. Larson, Joel Kaufman, Michael E. Rosenfeld, Xia Yang, Jesus A. Araujo

“…Consistently, DEP treatment of HepG2 cells led to increased gluconeogenesis and glycogenolysis indicating the ability of the in-vitro approach to model effects induced by DE in vivo. As an example, while gene network analysis of DE livers identified phosphoenolpyruvate carboxykinase 1 (Pck1) as a key driver gene of DE response, DEP treatment of HepG2 cells resulted in increased mRNA expression of Pck1 and glucose production, the latter replicated in mouse primary hepatocytes. …”
Get full text

A single-cell transcriptomic atlas of human lens epithelium: identification and functional insights into lens stem/progenitor cells by Yuzhou Gu, Lu Chen, Shuying Chen, Yuhao Wu, Shengjie Hao, Feiyin Sheng, Jiali Yuan, Zhenwei Qin, Di Wu, Yu Han, Zengying Yao, Zhijian Chen, I. Michael Wormstone, Yibo Yu, Junbin Qian, Qiuli Fu, Ke Yao

“…The 3 sub groups were labelled early, mid and late LECs and corresponded to stage 1, 3 and 4 in the path. While cell population demographics remained stable with age, transcriptomic changes in LECs were observed, including weaker intercellular crosstalk and adhesion, and fewer TACs in S phase. …”
Get full text

The role of JPT1 in hepatocellular carcinoma: tumor progression, microtubule dynamics regulation, and potential mechanisms within the immune microenvironment by Yipin Lu, Peng Xu, Sha Li, Jie Yao

“…Differentially expressed gene (DEG) analysis, functional enrichment analysis (GSEA and KEGG), and spatial transcriptomics were utilized to explore the biological functions and mechanisms of JPT1 in tumor biology. …”
Get full text

Identification of differentially expressed genes and proteins related to diapause in Lymantria dispar: Insights for the mechanism of diapause from transcriptome and proteome analys... by Qing Xie, Xiaofan Ma, Yafei Li, Wenzhuai Ji, Fengrui Dou, Xiue Zhu, Juan Shi, Yixia Cao

“…We performed bioinformatics analysis on four Asian populations of spongy moth and one Asian-European hybrid population through a transcriptome analysis combined with proteomics. …”
Get full text

Comparative transcriptomics reveals the key pathways and genes of cadmium accumulation in the high cadmium-accumulating rice (Oryza Sativa L.) line by Huan Yang, Haiying Yu, Shengwang Wang, Huagang Huang, Daihua Ye, Xizhou Zhang, Tao Liu, Yongdong Wang, Zicheng Zheng, Tingxuan Li

“…Here an in-depth exploration was performed via transcriptome analysis with 2919 and 2563 differentially expressed genes (DEGs) in H8 and N4 identified, respectively. …”
Get full text

Elucidation of fruit cracking mechanism in bael [Aegle marmelos (L.) Correa.] using physico-biochemical and de novo transcriptomic approaches by Vasanth Vinayak Vara Prasad, V.B. Patel, M.K. Dhakar, Bikash Das, Sujit Kumar Bishi, V.P. Bhadana, G.P. Mishra, Vishal Mhetre, S.K. Singh, Vishal Nath, Ram Asrey, Devendra Pandey

“…Three genotypes from each category were selected for further analysis. Biochemical profiling revealed that total flavonoids, antioxidants, vanillic acid and soluble carbohydrates were predominant in the cracking-susceptible genotypes, while calcium and boron levels were significantly lower in these genotypes. …”
Get full text

Effect of GR24 on the growth and development of licorice under low phosphorus stress by Yuting Jing, Man Li, Yong Wu, Chengming Zhang, Chengshu Qiu, Hengming Zhao, Li Zhuang, Hongling Liu

“…Under P2, increases were noted in isoliquiritigenin, liquiritigenin, and liquiritin levels. Transcriptome analysis revealed differential gene, with 137 and 270 genes up-regulated and 77 and 294 genes down-regulated in the P3 and P2 treatments, respectively. …”
Get full text

Redefining the high variable genes by optimized LOESS regression with positive ratio by Yue Xie, Zehua Jing, Hailin Pan, Xun Xu, Qi Fang

“…Abstract Background Single-cell RNA sequencing allows for the exploration of transcriptomic features at the individual cell level, but the high dimensionality and sparsity of the data pose substantial challenges for downstream analysis. …”
Get full text

Effect of Dead-Cell <i>Limosilactobacillus ingluviei</i> on Hematological Parameters and Jejunal Transcriptome Profile in Calves During the Weaning Period by Chao Ban, Supreena Srisaikham, Xingzhou Tian, Pipat Lounglawan

“…Transcriptomic analysis identified 76 differentially expressed genes (DEGs), with significant upregulation of genes involved in fatty acid metabolism (FABP1), intestinal barrier function (B4GALNT2), and detoxification (GSTA1), alongside downregulation of immune response regulation (FCRLA, FCRL4). …”
Get full text

Histological observation, transcriptome and methylome analyses reveal the dynamic changes during gonadal differentiation of spotted sea bass, Lateolabrax maculatus by Lingyu Wang, Haishen Wen, Xin Qi, Kaiqiang Zhang, Donglei Sun, Xueqi Li, Shaosen Yang, Yun Li

“…This study employed histology, RNA-Seq, and whole genome bisulfite sequencing (WGBS) to investigate early gonadal differentiation. Histological analysis revealed that testicular differentiation commenced before 120 days post-hatching (dph), while ovarian differentiation appeared before 180 dph. …”
Get full text

Transcriptomic profiles of Crandell-Rees feline kidney cells infected with Varicellovirus felidalpha-1 (FHV-1) field and vaccine strains by Emily Kwan, Alistair R. Legione, Carol A. Hartley, Joanne M. Devlin

“…Genes encoding histone proteins were upregulated, while genes involved in cell adhesion and migration processes were downregulated during infections with FHV-1. …”
Get full text

Deep RNA sequencing of pectoralis muscle transcriptomes during late-term embryonic to neonatal development in indigenous Chinese duck breeds. by Chunhong Zhu, Weitao Song, Zhiyun Tao, Hongxiang Liu, Wenjuan Xu, Shuangjie Zhang, Huifang Li

Get full text

Comparative transcriptomic and hormonal analyses reveal potential regulation networks of adventitious root formation in Metasequoia glyptostroboides Hu et Cheng by Yuping Xiong, Xiaohong Chen, Junyu Liu, Yuan Li, Zhan Bian, Xinhua Zhang, Songjun Zeng, Jaime A. Teixeira da Silva, Guohua Ma

“…Transcriptomic analysis showed the significant up- or down-regulation of differentially expressed genes (DEGs) associated with plant hormone signal transduction and the phenylpropanoid biosynthesis pathway in response to 2/5-strength WPM. …”
Get full text

Decoding the striatum of drug-naive patients with obsessive-compulsive disorder: a transcriptome and longitudinal functional magnetic resonance imaging study by Yiding Han, Haohao Yan, Xiaoxiao Shan, Huabing Li, Feng Liu, Ping Li, Dongsheng Lv, Jingping Zhao, Wenbin Guo

“…Associations between gene expression patterns and altered information flow patterns in SSs were examined, where information flow was measured using EC, followed by enrichment analysis of relevant genes. While no significant alterations were observed in the patients’ striata in whole-brain statistical analyses, significant changes in DC, FC, and EC were identified in SSs pre- and post-treatment. …”
Get full text

Transcriptome-wide regulation of folate on neural mRNA m6A methylome via carbon metabolism in Drosophila and mammals by Anrui Liu, Zhengyi Huo, Zihe Xu, Sisi Liu, Yuting Jiao, Rui Li, Yi Lu, Meng Yang, Jia Huang, Chen Huang, Xiaoyun Wang

Get full text

Mitochondrial transplantation normalizes transcriptomic and proteomic shift associated with ischemia reperfusion injury in neonatal hearts donated after circulatory death by Ilias P. Doulamis, Aspasia Tzani, Victor S. Alemany, Rio S. Nomoto, Aybuke Celik, Dominic P. Recco, Mossab Y. Saeed, Alvise Guariento, Jorge Plutzky, Sitaram M. Emani, Pedro J. del Nido, James D. McCully

“…Pathway analysis showed that ATP binding, voltage-gated K channel activity involved in cardiac cell muscle contraction and ribosomal RNA biogenesis were upregulated in the mitochondrial transplantation group, while mitochondria were the predicted source. …”
Get full text

Transcriptomic analyses reveal new genes and networks response to H5N1 influenza viruses in duck (Anas platyrhynchos) by Yin-hua HUANG, Hua-peng FENG, Li-ren HUANG, Kang YI, En-guang RONG, Xiao-yun CHEN, Jian-wen LI, Zeng WANG, Peng-yang ZHU, Xiao-juan LIU, Xiao-xue WANG, Jia-xiang HU, Xin LIU, Hua-lan CHEN, Jun WANG, Ning LI

“…., A/goose/Hubei/65/05, GS/65) are weakly pathogenic, while the others (i.e., A/duck/Hubei/49/05, DK/49) are highly pathogenic to their natural hosts. …”
Get full text

A comparison of the large‐scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China by Lingzhen Cao, Na Wang

Get full text