Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling by The exRNAQC Consortium

“…No study to date has systematically tested pre-analytical variables affecting transcriptome-wide exRNA analysis. By evaluating their impact on deep transcriptome profiling of microRNAs and mRNAs in blood plasma or serum, we compared ten blood collection tubes, three blood processing time intervals, and eight RNA purification methods. …”
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Comparative analysis of two stored sweet potato varieties using integrated transcriptomics and metabolomics by Xinyi Feng, Jinhua Zuo, Yunxiang Wang, Chunmei Bai, Shaoqing Chen, Lili Ma, Xuelian He, Jiejie Tao, Shiyu Liu, Yiting Ren, Demei Meng, Yanyan Zheng

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Comprehensive sex- and tissue-specific transcriptome of the destructive invasive pest Tuta absoluta adults by Zhiwei Kang, Aoli Lin, Mengqi Ji, Shizhao Jing, Zichao Song, Zhenxaing Li, Limei Song, Jianghua Sun, Cheng Qu

“…Taken together, this transcriptomic data not only contribute to the molecular investigations about olfactory perception of T. absoluta, but also provided important information to developing innovative controlling methods based on the olfaction process of T. absoulta.…”
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Evaluating the response of Schizothorax prenanti to ammonia nitrogen stress using computer vision and transcriptomics by Yinhua Zhou, He Gao, Hejiao Li, Tianyi Shen, Yifan Yao, Zhilei Wang, Yuting Duan, Junting Li, Suxing Fu, Shidong Liu, Rongrong Liao, Haiping Liu, Luo Lei, Chaowei Zhou

“…This study, for the first time, combines behavioral, histological, biochemical, and transcriptomic analyses to explore its response to ammonia nitrogen stress. …”
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Transcriptomic insights into the molecular mechanism of abietic acid promoting growth and branching in Armillaria gallica by Chun Luo, Yu Song, Lina Meng, Yajie Cheng, Huiping Dai, Yanming Qiao, Xiuchao Xie

“…This study investigates the effects of abietic acid on A. gallica growth and branching using phenotypic analysis and transcriptomic approaches to uncover underlying molecular mechanisms. …”
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Complete genome and transcriptome datasets of Streptococcus salivarius strains from healthy Korean subjects by Eun-Young Jang, Ji-Hoi Moon, Jae-Hyung Lee

“…While research on S. salivarius has primarily focused on strains originating from non-Asian populations, particularly New Zealand, with some studies also reporting European strains, research on strains originating from Korea has been notably lacking. This dataset provides the complete genome sequences and transcriptomic profiles of 12 S. salivarius strains isolated from healthy Korean individuals. …”
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Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data by Jiawen Hou, Wei Zhao, Qing Nie

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Characterization of 3,3′-iminodipropionitrile (IDPN) damaged utricle transcriptome in the adult mouse utricle by Mengyao Tian, Mengyao Tian, Jingyuan Huang, Jingyuan Huang, Hairong Xiao, Hairong Xiao, Pei Jiang, Pei Jiang, Xiangyu Ma, Xiangyu Ma, Yanqin Lin, Yanqin Lin, Xujun Tang, Xujun Tang, Yintao Wang, Yintao Wang, Mingchen Dai, Mingchen Dai, Wei Tong, Wei Tong, Zixuan Ye, Zixuan Ye, Xia Sheng, Xia Sheng, Renjie Chai, Renjie Chai, Renjie Chai, Renjie Chai, Renjie Chai, Renjie Chai, Shasha Zhang, Shasha Zhang

“…We found 1,165 upregulated genes and 1,043 downregulated genes in IDPN damaged utricles, and identified that NF-κB pathway and TNF pathway may play important roles in IDPN damage model. Our study provides details of transcriptome of IDPN utricle damage model for further study of vestibular dysfunction.…”
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Non-human primate seasonal transcriptome atlas reveals seasonal changes in physiology and diseases by Junfeng Chen, Kousuke Okimura, Liang Ren, Yusuke Nakane, Tomoya Nakayama, Yang Chen, Kai Fukawa, Soutarou Sugiyama, Takayoshi Natsume, Naoko Suda-Hashimoto, Mayumi Morimoto, Takako Miyabe-Nishiwaki, Takao Oishi, Yuma Katada, Manhui Zhang, Kohei Kobayashi, Shoko Matsumoto, Taiki Yamaguchi, Ying-Jey Guh, Issey Takahashi, Taeko Nishiwaki-Ohkawa, Daiki X. Sato, Yoshiharu Murata, Kenta Sumiyama, Atsushi J. Nagano, Hiroo Imai, Takashi Yoshimura

“…We find seasonal changes in plasma metabolites and hormones. Transcriptome analysis identifies sex differences in seasonally oscillating genes (SOGs) in all tissues studied, and we generate the web database ‘Non-Human Primate Seasonal Transcriptome Atlas (NHPSTA).’ …”
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Whole blood transcriptome profile identifies motor neurone disease RNA biomarker signatures by Sulev Kõks, Sulev Kõks, Karin Rallmann, Mari Muldmaa, Mari Muldmaa, Jack Price, Abigail L. Pfaff, Abigail L. Pfaff, Pille Taba

“…Blood-based whole transcriptomic analysis can reliably differentiate MND patients from controls and can provide useful information for the clinical management of the disease and clinical trials.…”
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Dishevelled-1 regulates global transcriptomic changes and associates with ETS1 transcription factor by Dalia Martinez-Marin, Monica Sharma, Jenna C. van Wunnik, Flávia Sardela de Miranda, Geetha Priya Boligala, Ella C. Jull, Grace C. Stroman, Rachel L. Babcock, Kevin Pruitt

“…We show here that modulation of DVL1 expression globally affects the transcriptomic landscape. Additionally, analysis of DVL1 ChIP-sequencing allowed us to map genome-wide binding sites, revealing the extensive reach of DVL1 binding. …”
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Exploring the dynamic pathogenesis of Parkinson's disease by case-control and longitudinal blood transcriptome analyses by Gang Xue, Gang Wang, Qianqian Shi, Hui Wang, Bo-Min Lv, Min Gao, Xiaohui Niu, Hong-Yu Zhang

“…Given the fact that transcriptional changes in blood can provide insightful clues for PD pathogenesis, we performed case-control and longitudinal whole blood transcriptome analyses to identify the signature genes underlying the hypothesized dynamic pathogenesis of PD. …”
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Ulmus minor response to Dutch elm disease: de novo transcriptome assembly and annotation by V. Chano, J. Sobrino-Plata, C. Martínez-Arias, C. Collada, J. Rodríguez-Calcerrada, J. A. Martín

“…In this work, a de novo transcriptome assembly of Ulmus minor in response to ONU is presented. …”
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Seasonal transcriptome profile across three different tissues of the Andean Killifish Orestias ascotanensis by Rodrigo Maldonado-Agurto, Elvis Acevedo, Vinicius Maracaja-Coutinho, Martin Montecino

“…These conditions make it an excellent model for studying high-altitude fish biology. However, the transcriptomic responses of O. ascotanensis to seasonal acclimation remain unexplored. …”
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Physiological response and transcriptomic analysis of red-fleshed apple seedlings to low temperature stress by LingYu Meng, Rui Zhang, YanPing Wei, Tingting Gu, Jiahao Zhao, Zijing Chen, Zongying Zhang, Nan Wang, Xuesen Chen, Wenjun Liu

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Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients by Mirko Signorelli, Mitra Ebrahimpoor, Olga Veth, Kristina Hettne, Nisha Verwey, Raquel García‐Rodríguez, Christa L Tanganyika‐deWinter, Luz B Lopez Hernandez, Rosa Escobar Cedillo, Benjamín Gómez Díaz, Olafur T Magnusson, Hailiang Mei, Roula Tsonaka, Annemieke Aartsma‐Rus, Pietro Spitali

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Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer by Mahnoor Naseer Gondal, Hafiz Muhammad Umer Farooqi

“…Recent developments in single-cell transcriptome profiling methods have revealed surprising levels of expression variability among seemingly homogeneous cells, suggesting the existence of many more cell types than previously estimated. …”
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Transcriptomics profiling of Parkinson’s disease progression subtypes reveals distinctive patterns of gene expression by Carlo Fabrizio, Andrea Termine, Carlo Caltagirone

“…Conclusion This study provides novel information regarding the transcriptomics profiles of PD progression subtypes, which may foster precision medicine with relevant indications for a finer-grained diagnosis and prognosis.…”
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Multiple Transcriptomic Networks Regulate the Callus Development Process in <i>Panax ginseng</i> by Jaewook Kim, Jung-Woo Lee, Ick-Hyun Jo

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Transcriptome profile of early matured Macrobrachium rosenbergii (Giant Freshwater Prawn) from Taiwan by Sofia Priyadarsani Das, Yu-Ru Lin, Yu-Sheng Wu, Chun-Hung Liu, Yeh-Fang Hu, Fan-Hua Nan

“…The information produced will be used as a foundation for transcriptome-based genetic research, which will provide fresh perspectives on the species’ precocious puberty and diverse length distribution of this species.…”
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