Characterization of Mucosal Immune-Related lncRNAs and mRNAs in a Mouse Model of Allergic Conjunctivitis by Zhang H, Zhang H, Leng Q, Zheng YJ

“…Transcriptomic analysis revealed significant differences in mRNAs and lncRNAs expression between AC and control groups. …”
Get full text

Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data by Joshua Chuah, Carmalena V. Cordi, Juergen Hahn, Jennifer M. Hurley

“…Abstract Background The circadian clock is a central driver of many biological and behavioral processes, regulating the levels of many genes and proteins, termed clock controlled genes and proteins (CCGs/CCPs), to impart biological timing at the molecular level. While transcriptomic and proteomic data has been analyzed to find potential CCGs and CCPs, multi-omic modeling of circadian data, which has the potential to enhance the understanding of circadian control of biological timing, remains relatively rare due to several methodological hurdles. …”
Get full text

Machine learning-based transcriptmics analysis reveals BMX, GRB10, and GADD45A as crucial biomarkers and therapeutic targets in sepsis by Yanwei Cheng, Haoran Peng, Qiao Chen, Lijun Xu, Lijie Qin

Get full text

Integrated mRNA and miRNA Analysis Reveals Layer-Specific Mechanisms of Antler Yield Variation in Sika Deer by Derui Zhao, Zhen Zhang, Qianghui Wang, Heping Li

“…In particular, genes such as <i>FBP2</i>, <i>TPT1</i>, <i>TFRC</i>, <i>ZEB1</i>, and <i>PHOSPHO1</i> were upregulated in high-yield deer across specific tissue layers, while <i>NFATC2</i> was downregulated in these high-yield deer. …”
Get full text

Transcriptomic HEPN1 signatures predict treatment response in low grade glioma by Lei Jiao, Shuhua Fang, Jianbo Zhang

“…By leveraging comprehensive single-cell transcriptomic approaches, this investigation seeks to establish HEPN1 as a pivotal biomarker while examining its utility in directing ferroptosis-targeted therapeutic interventions for glioma patients. …”
Get full text

SpaMask: Dual masking graph autoencoder with contrastive learning for spatial transcriptomics. by Wenwen Min, Donghai Fang, Jinyu Chen, Shihua Zhang

“…Recent advancements in spatial resolved transcriptomics (SRT) have enabled the analysis of gene expression while preserving the spatial context within tissues. …”
Get full text

Effects of graphene on morphology, microstructure and transcriptomic profiling of Pinus tabuliformis Carr. roots. by Xiao Zhang, Huifen Cao, Haiyan Wang, Runxuan Zhang, Haikuan Jia, Jingting Huang, Jianguo Zhao, Jianzhong Yao

Get full text

ABA-induced alternative splicing drives transcriptomic reprogramming for drought tolerance in barley by Anna Collin, Hubert Matkowski, Ewa Sybilska, Asmarany Biantari, Oliwia Król, Agata Daszkowska-Golec

“…Photosynthetic parameters, including photosystem II activity, electron transport rate, and the number of active reaction centers, were preserved in ABA-pretreated plants compared with drought-only plants. Transcriptomic analysis revealed that ABA pre-treatment primed plants for faster activation of stress-responsive pathways, with enhanced expression of genes related to chromatin modifications, RNA metabolism, and ABA signaling during drought. …”
Get full text

Dietary inulin supplementation modifies significantly the liver transcriptomic profile of broiler chickens. by Natalia Sevane, Federica Bialade, Susana Velasco, Almudena Rebolé, Maria Luisa Rodríguez, Luís T Ortiz, Javier Cañón, Susana Dunner

“…Quantitative real-time PCR analysis validated the microarray expression results for five out of seven genes tested. …”
Get full text

Characterizing differences in the muscle transcriptome between cattle with alternative LCORL-NCAPG haplotypes by Fernanda Martins Rodrigues, Leif E. Majeres, Anna C. Dilger, Joshua C. McCann, Christopher J. Cassady, Dan W. Shike, Jonathan E. Beever

“…To further understand the molecular mechanism responsible for the phenotypic changes associated with this locus, twenty-four Charolais-sired calves were selected for muscle transcriptome analysis based on alternative homozygous LCORL-NCAPG haplotypes (i.e., 12 “QQ” and 12 “qq”, where “Q” is a haplotype harboring variation associated with increased growth). …”
Get full text

Transcriptomic profiling and bioinformatic insights into myocardial injury following aneurysmal subarachnoid hemorrhage by Zuoli Wu, Zuoli Wu, Wenbo He, Weihao Ye, Shang Xu, Shengwei Wei, Baozi Huang, Pingping Li, Yanyan Tang, Chao Qin, Ying Liu, Ziming Ye

“…Bioinformatic analysis suggests these genes may play critical roles in the pathogenesis of aSAH-MI.…”
Get full text

Proteomics and transcriptomics combined reveal specific immunological markers in autoimmune thyroid disease by Xia Chen, Hui Chen

“…Through the combined analysis of transcriptomics and proteomics, key genes IGHG3, ISG15, and ZNF683 were identified. …”
Get full text

Comparative phenotypic, physiological, and transcriptomic responses to drought and recovery in two Fraxinus species by Tae-Lim Kim, Hyemin Lim, Kyungmi Lee, Michael Immanuel Jesse Denison, Sathishkumar Natarajan, Changyoung Oh

“…Transcriptome analysis revealed that photosynthesis and enzyme activity were the most responsive to drought and recovery, as shown by Gene Ontology term analysis. …”
Get full text

Race-related host and microbe transcriptomic signatures in triple-negative breast cancer by Roshan Kumar, Susan Duyar-Ayerdi, Aishwarya Sundaresan, Vinodh Srinivasasainagendra, Chandra Sekhar Pedamallu, Michael Behring, Darshan Shimoga Chandrashekar, Isam-Eldin Eltoum, Sooryanarayana Varambally, Hemant K. Tiwari, Sadeep Shrestha, Paul L. Auer, Lubna N. Chaudhary, John R. Kirby, Clayton Yates, Upender Manne, Akinyemi I. Ojesina

“…Abstract Triple-negative breast cancer (TNBC) shows racial disparities, with higher incidence in women of African ancestry (AA) compared to European ancestry (EA). Meta-transcriptomic analysis of TNBC tumor tissues from AA (n = 17) and EA (n = 19) subjects revealed distinct microbial landscapes. …”
Get full text

Transcriptome and metabolome profiling reveal the inhibitory effects of food preservatives on pathogenic fungi by Zhenxia Shi, Ni Zhan, Ming Ma, Zhen Wang, Xunyou Yan, Rumeng Li, Xuejuan Liu

“…Similarly, 0.5% sec-butylamine, 1.0% citric acid, and 0.6% potassium sorbate completely inhibited A. alternata, while 1.0% sec-butylamine, 1.2% citric acid, and 0.8% potassium sorbate completely inhibited T. funiculosus. …”
Get full text

Combining Transcriptomics and Proteomics to Screen Candidate Genes Related to Bovine Birth Weight by Xiuyuan Wang, Ruili Liu, Zhenpeng Chen, Renzheng Zhang, Yanfang Mei, Xiuping Miao, Xuejin Bai, Yajuan Dong

“…Furthermore, we identified 53 genes and proteins exhibiting significant co-expression across both transcriptomic and proteomic datasets; among these, 40 were co-upregulated, 8 co-downregulated, while 5 displayed upregulation at the protein level despite downregulation at the mRNA level. …”
Get full text

New insights into the transcriptomic profile during the late stages of chicken embryonic development by Di Zhao, Yifan Shi, Jiatai Deng, Bolin Zhong, Yuanyuan Zeng, Qingyuan Ouyang, Haihan Zhang, Zehe Song, Xi He

“…While comprehensive transcriptomic characterization of muscle development during the hatching stage remains limited, we conducted an integrated analysis of coding and non-coding RNA profiles in the pectoral muscles of Arbor Acres (AA) broilers and TaoYuan (TY) chickens at embryonic days 17 (E17), 19 (E19), and 21 (E21). …”
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

“…Transcriptome analysis revealed that 485 and 627 differentially expressed genes (DEGs) were determined in the brain and liver from sea bass after transportation stress, respectively. …”
Get full text

A Transcriptomic Dataset of Embryonic Murine Telencephalon of Fmr1-Deficient Mice by Sara Ebrahimiazar, Takako Kikkawa, Yohei Minakuchi, Satoshi Miyashita, Shyu Manabe, Mikio Hoshino, Atsushi Toyoda, Noriko Osumi

Get full text

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models by Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, Nir Yosef

“…In this manuscript, we demonstrate that our previously developed method, scVI, provides an effective and fully probabilistic approach for joint representation and analysis of scRNA‐seq data, while accounting for uncertainty caused by biological and measurement noise. …”
Get full text