Characterization of transcriptome remodeling during cambium formation identifies MOL1 and RUL1 as opposing regulators of secondary growth. by Javier Agusti, Raffael Lichtenberger, Martina Schwarz, Lilian Nehlin, Thomas Greb

“…By combining this system with laser capture microdissection, we characterized transcriptome remodeling in a tissue- and stage-specific manner and identified series of genes induced during different phases of cambium formation. …”
Get full text

Integrating explainable machine learning and transcriptomics data reveals cell-type specific immune signatures underlying macular degeneration by Khang Ma, Hosei Nakajima, Nipa Basak, Arko Barman, Rinki Ratnapriya

“…Here, we develop an explainable machine-learning pipeline (ML) using transcriptome data of 453 donor retinas, identifying 81 genes distinguishing AMD from controls (AUC-ROC of 0.80, CI 0.70–0.92). …”
Get full text

Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies by Brandon Robin, Alexandre Baillez, Servane Le Guillouzer, Cécile Lecoeur, Florent Sebbane, Sébastien Bontemps-Gallo

“…Abstract Transcriptomics is key to understanding how bacterial pathogens adapt and cause disease, but remains constrained by cost, technical, and biosafety issues, especially for highly virulent and/or regulated pathogens. …”
Get full text

Regulation of ethyl ester synthesis in two apple (Malus domestica) cultivars: Insights from integrated metabolomic and transcriptomic analyses by Fukuyo Tanaka, Ryoichi Yano, Keiki Okazaki, Hikari Kuchikata, Jimpachi Masuda, Satoshi Kasai, Miho Tatsuki

Get full text

Single-cell transcriptome analysis identifies MIF as a novel tumor-associated neutrophil marker for pancreatic ductal adenocarcinoma by Yan Zeng, Jiaping Yu, Yutong Chen, Juan Zhuang, Xinyue Liang, Yaning Li, Shili Chen, Wenzheng Pang, Linjuan Zeng

Get full text

Cross-species single-cell transcriptomic atlas of retinal photoreceptors reveals molecular signatures underlying color vision adaptation by Zhibin Li, Chengkai Yan, Yubao Lu, Yaqing Shu, Shilin Wu, Xi Cheng, Yuge Wang, Shishi Shen, Hui Yang, Gang Cao, Jianping Ji, Liangming Zhang, Jian Sun, Dongchang Xiao, Shasha Li, Wei Qiu

Get full text

Utilizing physiologies, transcriptomics, and metabolomics to unravel key genes and metabolites of Salvia miltiorrhiza Bge. seedlings in response to drought stress by Yu Zhang, Hong Zhang, Yuru Zhang, Di Wang, Xue Meng, Juan Chen

“…Here, we studied the effects of drought stress on the different parts of S. miltiorrhiza seedlings through physiological, transcriptomic, and metabolomics analyses, and identified key genes and metabolites related to drought tolerance. …”
Get full text

Integrating genome and transcriptome-wide data to explore the expression dynamics of TCP genes in Pisum sativum under salt stress by Song Fangyuan, Li Yong, Jin Huang, Guo Zhiyue, Deng Wen

Get full text

Integrated transcriptomic and metabolomic analyses reveal critical gene regulatory network in response to drought stress in Dendrobium nobile Lindl by Chaoyan Lv, Ya He, Zaiqian Jiang, Wenjia Hu, Mei Zhang

“…Global transcriptomic changes were detected in Dendrobium under different drought stress conditions. …”
Get full text

Inflammation-associated molecules in the glomerular-endothelium in mild IgA-nephropathy patients identified by single-cell and spatial transcriptome by Kumi Hasegawa, Nagako Kawashima, Ayako Kawabata, Megumi Sakakura, Naoki Onoda, Takashi Sano, Itaru Urakawa, Masahiro Matsubara, Shokichi Naito

“…We conduct single-cell and spatial transcriptomic analysis using human specimens with mild IgA-N compared with normal. …”
Get full text

Integrated metabolomic and transcriptomic analysis highlight the flavonoid response to antioxidant activity and Aspergillus flavus resistance in peanut seed coats by Xuejie Zhao, Minghui Xing, LiJing Zhang, Suoyi Han, Xinyou Zhang, Jinyong Huang

“…Conclusions This study provides novel insights into the biochemical mechanisms underlying peanut resistance to A. flavus, while also supporting the valorization of peanut by-products and the breeding of resistant cultivars.…”
Get full text

Organic fertilizer substitution altered the waxy maize grain quality and aroma volatiles formation by the integrated transcriptomic and metabolomic analyses by Xiaoqiang Zhao, Qiang Chai, Wen Yin, Hong Fan, Wei He, Cai Zhao

“…The interaction network analysis further revealed the complexity of quality and aroma formation. The findings provide valuable insights into grain quality and volatiles formation during waxy maize grain development under organic fertilizer substitution.…”
Get full text

Transcriptomic and Metabolic Analysis Reveals Genes and Pathways Associated with Flesh Pigmentation in Potato (<i>Solanum tuberosum</i>) Tubers by Man Li, Yuting Xiong, Xueying Yang, Yuliang Gao, Kuihua Li

“…These findings provide potential molecular targets for breeding programs focused on enhancing tuber color.…”
Get full text

Transcriptome signature for multiple biotic and abiotic stress in barley (Hordeum vulgare L.) identifies using machine learning approach by Bahman Panahi

“…This study utilizes machine learning to analyze transcriptomic data from 515 RNA-seq profiles across 18 independent studies, covering eleven abiotic and three biotic stress types. …”
Get full text

Single‐Nucleus and Spatial Transcriptome Profiling Delineates the Multicellular Ecosystem in Hepatocellular Carcinoma After Hepatic Arterial Infusion Chemotherapy by YeXing Huang, ZeFeng Du, ZhiCheng Lai, DongSheng Wen, LiChang Huang, MinKe He, ZiChao Wu, HuiFang Li, HanYue OuYang, WenChao Wu, Anna Kan, Ming Shi

“…Here, we collected tumor samples from treatment‐naïve primary and post‐HAIC HCC, and integrated single‐nucleus RNA sequencing with spatial transcriptomics to characterize the tumor ecosystem in the post‐HAIC HCC. …”
Get full text

Integrated Metabolomic and Transcriptomic Analysis Reveal the Production Mechanism of Semicarbazide in <i>Macrobrachium rosenbergii</i> Under Urea Conditions by Jun Li, Di Wang, Shengjun Chen, Fangfang Gao, Chunsheng Li, Yang Feng, Jianchao Deng

“…Compared to traditional single-omics approaches, this method provided a comprehensive analysis of gene–metabolite interactions, revealing the mechanism of endogenous production of SEM in <i>M. rosenbergii.…”
Get full text

De Novo Assembly, Characterization and Comparative Transcriptome Analysis of the Mature Male and Female Gonads in <i>Acrossocheilus parallens</i> by Weiqian Liang, Lanyuan Liu, Dingxian Chen, Kaifeng Wang, Shengyue Lin, Weijian Chen, Sixun Li, Binhua Deng, Qiang Li, Chong Han

“…In this research, the gonadal transcriptome sequencing data of female and male <i>A. parallens</i> were first analyzed and compared. …”
Get full text

Integrative Transcriptomic and Metabolomic Analysis Reveals Quinoa Leaf Response Mechanisms to Different Phosphorus Concentrations During Filling Stage by Hongxin Wang, Hanxue Li, Xiaorong Li, Qianchao Wang, Junna Liu, Ping Zhang, Heng Xie, Li Li, Peng Qin

“…Therefore, we conducted metabolome and transcriptome analyses on quinoa leaves during the filling stage, subjecting plants to different doses of phosphorus fertilizer. …”
Get full text

Caloric restriction mimetic 2-deoxyglucose alters metabolic and transcriptomic phenotype in association with changes in chromatin accessibility in human astrocytes by Matthew Spencer, Jacqueline R. Kulbe, Vikram Venkatesh, Anna Laird, Mary Ford, Sydney O’Brien, Ali Boustani, Johannes C. M. Schlachetzki, Jerel Adam Fields

Get full text

Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration. by Cláudia Raposo de Magalhães, Kenneth Sandoval, Ferenc Kagan, Grace McCormack, Denise Schrama, Raquel Carrilho, Ana Paula Farinha, Marco Cerqueira, Pedro M Rodrigues

“…These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.…”
Get full text