A collaborative network analysis for the interpretation of transcriptomics data in Huntington’s disease by Ozan Ozisik, Nazli Sila Kara, Tooba Abbassi-Daloii, Morgane Térézol, Elsa C. Kuijper, Núria Queralt-Rosinach, Annika Jacobsen, Osman Ugur Sezerman, Marco Roos, Chris T. Evelo, Anaïs Baudot, Friederike Ehrhart, Eleni Mina

“…We analyzed a Huntington’s disease transcriptomics dataset using six network-based methods in a collaborative way. …”
Get full text

The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback by Man Luo, Junjie Zhao, Juha Merilä, Rowan D. H. Barrett, Baocheng Guo, Juntao Hu

“…Conclusions Our results suggest a nuanced relationship between epigenomic and transcriptomic processes, with alignment at the genome-wide level masking relatively independent effects of different molecular mechanisms on ecotype divergence at the gene level.…”
Get full text

Intergeneric and interspecific relationships in tribe Ricineae revealed by phylogenomics of the plastome and transcriptome by Wen-Xiang Liu, Wen-Xiang Liu, Guo-Bo Li, Guo-Bo Li, Zhuo Zhou, Jia-Fu Chen, An-Min Yu, Ai-Zhong Liu, Bin Tian, Bin Tian, Jun-Wei Ye

“…The three genera formed a well-supported monophyletic lineage, confirmed by different genomic data using different methods. Discocleidion and Ricinus were supported to be closely related. …”
Get full text

A Guide to Basic RNA Sequencing Data Processing and Transcriptomic Analysis by Rowayna Shouib, Gary Eitzen, Rineke Steenbergen

“…RNA sequencing (RNA-Seq) has transformed transcriptomic research, enabling researchers to perform large-scale inspection of mRNA levels in living cells. …”
Get full text

Time course transcriptome changes in Shewanella algae in response to salt stress. by Xiuping Fu, Duochun Wang, Xiling Yin, Pengcheng Du, Biao Kan

Get full text

Integrated metabolomic and transcriptomic analysis provides insights into the browning of walnut endocarps by Yifeng Wang, Mingxia Wang, Yaonian Chen, Wenbin Hu, Shuling Zhao

“…In the present study, to elucidate the molecular mechanism of walnut endocarp browning, analyses of the ultrastructure, physiological characteristics, and transcriptomic and metabolomic data of walnut endocarps at different storage periods were performed. …”
Get full text

Organoids as powerful models of endometrium epithelium in transcriptomic, cellular and functional mimicry by Martina Ciprietti, Celine Bueds, Hugo Vankelecom, Joris Vriens

“…A comprehensive overview of the transcriptomic changes during the menstrual cycle is provided, as well as of the detailed comparison between the different cell populations of the endometrium and the endometrial organoid model. …”
Get full text

Spatial transcriptomics in autoimmune rheumatic disease: potential clinical applications and perspectives by Atsuko Tsujii Miyamoto, Hiroshi Shimagami, Atsushi Kumanogoh, Masayuki Nishide

“…In the field of rheumatology, the complex and elusive pathophysiology of diseases such as rheumatoid arthritis, systemic lupus erythematosus, and Sjögren’s syndrome remains a challenge for personalized treatment. Spatial transcriptomics provides insights into how different cell populations interact within disease foci, such as the synovial tissue, kidneys, and salivary glands. …”
Get full text

Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples by Wenyuan Yang, Hang Yu, Lian Tao, Hongjiang Xie

“…In this multidimensional regulatory study, we used transcriptome sequencing, cluster analysis, and weighted gene co-expression network analysis (WGCNA) to reveal that differentially expressed genes are enriched in multiple pathways affecting fruit acidity during apple development; malate dehydrogenase (MDH) affects the malic acid content of fruits of different varieties; and H⁺-ATPase (VHA) mainly regulates the content of vacuolar organic acids, which affects fruit acidity. …”
Get full text

RIDDEN: Data-driven inference of receptor activity from transcriptomic data. by Szilvia Barsi, Eszter Varga, Daniel Dimitrov, Julio Saez-Rodriguez, László Hunyady, Bence Szalai

“…We collected 14463 perturbation gene expression profiles for 229 different receptors. Using these data, we trained the RIDDEN model, which can effectively predict receptor activity for new bulk and single-cell transcriptomics datasets. …”
Get full text

Cross study transcriptomic investigation of Alzheimer’s brain tissue discoveries and limitations by Fernando Koiti Tsurukawa, Yixiang Mao, Cesar Sanchez-Villalobos, Nishtha Khanna, Chiquito J. Crasto, J. Josh Lawrence, Ranadip Pal

“…Abstract Developing effective treatments for Alzheimer’s disease (AD) likely requires a deep understanding of molecular mechanisms. Integration of transcriptomic datasets and developing innovative computational analyses may yield novel molecular targets with broad applicability. …”
Get full text

Identification of the Genomics and Transcriptomics Regulators of the DNA Damage Response in Breast Cancer by Mehdi Sadeghi, Mohammad Reza Karimi, Amir Hossein Karimi

Get full text

Integrated Metabolomic and Transcriptomic Analysis Revealed the Mechanism of BHPF Exposure in Endometrium by Xin Tan, Nengyong Ouyang, Wenjun Wang, Junting Qiu

“…Here, we investigated the effects of exposure to different concentrations of BHPF on endometrial cells and used integrated metabolomic and transcriptomic methods to elucidate the underlying molecular mechanisms. …”
Get full text

Single-Cell Transcriptome Analyses of Four Pain Related Genes in Osteosarcoma by Mesalie Feleke, Haiyingjie Lin, Yun Liu, Liang Mo, Emel Rothzerg, Dezhi Song, Jinmin Zhao, Wenyu Feng, Jiake Xu

Get full text

Long-Term Salinity-Responsive Transcriptome in Advanced Breeding Lines of Tomato by Monther T. Sadder, Ahmad Abdelrahim Mohamed Ali, Abdullah A. Alsadon, Mahmoud A. Wahb-Allah

Get full text

New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage by Éderson Akio Kido, José Ribamar Costa Ferreira Neto, Roberta Lane de Oliveira Silva, Valesca Pandolfi, Ana Carolina Ribeiro Guimarães, Daniela Truffi Veiga, Sabrina Moutinho Chabregas, Sérgio Crovella, Ana Maria Benko-Iseppon

“…The present report analyzes the sugarcane transcriptome under drought stress, using a combination of high-throughput transcriptome profiling by SuperSAGE with the Solexa sequencing technology, allowing the identification of potential target genes during the stress response.…”
Get full text

Transcriptome Profiling Identifies Key Regulators of Tuber Skin Color in Potato by Boshu Li, Shuo Wang, Jun Hu, Liping Jin, Jianfei Xu

“…The color of tuber skin exhibits remarkable diversity in potato (<i>Solanum tuberosum</i> L.) and is intricately associated with variance in anthocyanin accumulation across different varieties. The regulatory mechanisms governing this phenomenon are poorly understood. …”
Get full text

Transcriptome sequencing of Antheraea pernyi antennae for identification of olfactory-related genes by Xueting Liu, Shuwei Ma, Xinxue Zhang, Xue Li, Lei Nie, Guobao Wang

“…Results Based on the datasets, 1184 differently expressed genes (DEGs), including 484 upregulated and 700 downregulated genes, were identified by comparing the transcriptome profiles of the male and female antennae of A. pernyi. …”
Get full text

Transcriptome atlas of Striga germination: Implications for managing an intractable parasitic plant by Gilles Irafasha, Sylvia Mutinda, Fredrick Mobegi, Brett Hale, George Omwenga, Asela J. Wijeratne, Susann Wicke, Emily S. Bellis, Steven Runo

“…To further understand the genetic basis of the communication exchange between Striga and its host sorghum, we performed a comparative transcriptomic analysis. We sought to identify major transcriptomic changes that define the germination process in Striga and a set of genes that may contribute to the differences in germination rates. …”
Get full text

Single-cell transcriptomics for immune profiling of cerebrospinal fluid in neurological diseases by David Ramos-Vicente, Paola Monterosso, Oriol de Fàbregues, Oriol de Fàbregues, Gerard Roch, Miquel Vila, Miquel Vila, Miquel Vila, Miquel Vila, Jordi Bové

“…In this comprehensive review, we delve into the significant body of research on single-cell transcriptomics in cerebrospinal fluid (CSF) to understand neurological diseases with autoimmune, neurodegenerative, infectious, or oncogenic origins. …”
Get full text