Transcriptome Analysis Reveals Dynamic Fat Accumulation in the Walnut Kernel by Shuang Zhao, Xuemei Zhang, Yanping Su, Yilan Chen, Yang Liu, Meng Sun, Guohui Qi

“…The high-throughput transcriptome sequencing of walnut in different developmental stages has greatly enriched the current genomic available resources. …”
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Transcriptomic analysis of Phytophthora infestans races and evaluation of their pathogenicity on potato by Linmei Deng, Jianjun Hao, Jiawen Feng, Jing Zhao, Jian Dao, Gaihuan Xu, Kunyan Zhou, Yajin Xu, Wenping Wang, Shunhong Zhang, Chunjiang Liu, Meng Chen, Yanli Yang, Xia Liu

“…To explore the genetic mechanisms behind these, different physiological races of P. infestans were inoculated on potato leaves and assayed through transcriptomics combined with metabolic profiling methods. …”
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Transcriptomic regulation of juvenile-to-adult vegetative phase transition in grapevine by Yolanda Ferradás, Carolina Royo, José Miguel Martínez-Zapater, Diego Lijavetzky

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Unveiling unique metabolomic and transcriptomic profiles in three Brassicaceae crops by Liyong Zhang, Isobel A. P. Parkin

“…Interestingly, the responses of these three crops to different environmental stimuli vary to a great extent, but there is very limited knowledge about the molecular basis of these differential responses. …”
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Transcriptome analysis of bread wheat leaves in response to salt stress. by Nazanin Amirbakhtiar, Ahmad Ismaili, Mohammad-Reza Ghaffari, Raheleh Mirdar Mansuri, Sepideh Sanjari, Zahra-Sadat Shobbar

“…In the current study, the transcriptome of wheat leaves in an Iranian salt-tolerant cultivar (Arg) was investigated in response to salinity stress to identify salinity stress-responsive genes and mechanisms. …”
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SpaNorm: spatially-aware normalization for spatial transcriptomics data by Agus Salim, Dharmesh D. Bhuva, Carissa Chen, Chin Wee Tan, Pengyi Yang, Melissa J. Davis, Jean Y. H. Yang

“…SpaNorm is versatile and works equally well for multicellular and subcellular spatial transcriptomics data with relatively robust performance under different segmentation methods.…”
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Transcriptome analysis of Phytolacca americana L. in response to cadmium stress. by Yongkun Chen, Junkai Zhi, Hao Zhang, Jian Li, Qihong Zhao, Jichen Xu

“…In this study, the de novo sequencing of total RNA produced 53.15 million reads covering 10.63 gigabases of transcriptome raw data in cadmium (Cd)-treated and untreated pokeweed. …”
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Spatial Transcriptomics in Thyroid Cancer: Applications, Limitations, and Future Perspectives by Chaerim Song, Hye-Ji Park, Man S. Kim

“…Spatial transcriptomics (ST) is emerging as a powerful technology that transforms our understanding of thyroid cancer by offering a spatial context of gene expression within the tumor tissue. …”
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Deciphering plant transcriptomes: Leveraging machine learning for deeper insights by Bahman Panahi, Rasmieh Hamid, Hossein Mohammad Zadeh Jalaly

“…Plant transcriptomics is an important field for understanding the dynamics of gene expression, regulatory mechanisms and interactions underlying plant development and stress responses. …”
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Development of hop transcriptome to support research into host-viroid interactions. by Tine Pokorn, Sebastjan Radišek, Branka Javornik, Nataša Štajner, Jernej Jakše

“…These results provide a deep transcriptome of hop and the first insights into complex viroid-hop plant interactions.…”
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Single-cell transcriptomics analysis of the healing process of ligament rupture by Haibo Zhao, Jianbao Gong, Tengbo Yu, Yingze Zhang

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Dissection of tumoral niches using spatial transcriptomics and deep learning by Karla Paniagua, Yu-Fang Jin, Yidong Chen, Shou-Jiang Gao, Yufei Huang, Mario Flores

“…The pipeline consists in different stages that include normalization, spatial information integration, morphological feature extraction, gene expression quantification, single cell expression characterization, and tumor niche characterization. …”
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Comparative Transcriptome Analysis of Susceptible and Resistant Rutaceae Plants to Huanglongbing by Huihong Liao, Fuping Liu, Xi Wang, Hongming Huang, Qichun Huang, Nina Wang, Chizhang Wei

“…The transcriptome data showed that in the susceptible Ponkan Mandarin, there were 1519 upregulated genes and 700 downregulated genes, while in the resistant Punctate Wampee variety, there were 1611 upregulated genes and 1727 downregulated genes. …”
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Distinct transcriptome and traits of freshly dispersed Pseudomonas aeruginosa cells by Manmohit Kalia, Karin Sauer

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Transcriptomic Changes in Broiler Chicken Hypothalamus during Growth and Development by Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Połtowicz, Joanna Nowak, Dorota Wojtysiak, Natalia Derebecka, Joanna Wesoły, Katarzyna Ropka-Molik

“…The hypothalamic transcriptomes for 3- and 6-week-old cockerels were analysed using an RNA sequencing method in next-generation sequencing (NGS) technology. …”
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Integrated metabolomic and transcriptomic analysis of anthocyanin metabolism in wheat pericarp by Jiao Wang, Lei Sun, Bo Jiao, Pu Zhao, Tianyun Xu, Sa Gu, Chenmin Huo, Jianzhou Pang, Shuo Zhou

“…Abstract Background Wheat seeds display different colors due to the types and contents of anthocyanins, which is closely related to anthocyanin metabolism. …”
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A high-resolution anatomical atlas of the transcriptome in the mouse embryo. by Graciana Diez-Roux, Sandro Banfi, Marc Sultan, Lars Geffers, Santosh Anand, David Rozado, Alon Magen, Elena Canidio, Massimiliano Pagani, Ivana Peluso, Nathalie Lin-Marq, Muriel Koch, Marchesa Bilio, Immacolata Cantiello, Roberta Verde, Cristian De Masi, Salvatore A Bianchi, Juliette Cicchini, Elodie Perroud, Shprese Mehmeti, Emilie Dagand, Sabine Schrinner, Asja Nürnberger, Katja Schmidt, Katja Metz, Christina Zwingmann, Norbert Brieske, Cindy Springer, Ana Martinez Hernandez, Sarah Herzog, Frauke Grabbe, Cornelia Sieverding, Barbara Fischer, Kathrin Schrader, Maren Brockmeyer, Sarah Dettmer, Christin Helbig, Violaine Alunni, Marie-Annick Battaini, Carole Mura, Charlotte N Henrichsen, Raquel Garcia-Lopez, Diego Echevarria, Eduardo Puelles, Elena Garcia-Calero, Stefan Kruse, Markus Uhr, Christine Kauck, Guangjie Feng, Nestor Milyaev, Chuang Kee Ong, Lalit Kumar, MeiSze Lam, Colin A Semple, Attila Gyenesei, Stefan Mundlos, Uwe Radelof, Hans Lehrach, Paolo Sarmientos, Alexandre Reymond, Duncan R Davidson, Pascal Dollé, Stylianos E Antonarakis, Marie-Laure Yaspo, Salvador Martinez, Salvador Martinez, Richard A Baldock, Gregor Eichele, Andrea Ballabio

“…This digital transcriptome atlas, the Eurexpress atlas (http://www.eurexpress.org), consists of a searchable database of annotated images that can be interactively viewed. …”
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The transcriptomic fingerprint of cancer response to Tumor Treating Fields (TTFields) by Kerem Wainer-Katsir, Adi Haber, Hila Fishman, Lianghao Ding, Michael D. Story, Renfei Du, Ulf D. Kahlert, Laura Mannarino, Federica Mirimao, Monica Lupi, Maurizio D’Incalci, Gitit Lavy-Shahaf, Hila Ene, Roni Frechtel-Gerzi, Zeina Drawshy, Antonia Martinez-Conde, Eyal Dor-On, Yaara Porat, Moshe Giladi, Uri Weinberg, Yoram Palti

“…In the current research we performed whole transcriptome analysis across tumor types to identify pan-cancer responses to TTFields. …”
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Dynamic changes in the skin transcriptome for the melanin pigmentation in embryonic chickens by Dong Leng, Maosen Yang, Xiaomeng Miao, Zhiying Huang, Mengmeng Li, Jia Liu, Tao Wang, Diyan Li, Chungang Feng

“…Historically, research has concentrated primarily on specific developmental points or stages, but fewer studies have examined the entire transcriptome across the timeline of the development of the embryo integument. …”
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Transcriptomic characterization of transitioning cell types in the skin of Atlantic salmon by R. Ruiz Daniels, S. J. Salisbury, L. Sveen, P. R. Villamayor, R. S. Taylor, M. Vaadal, T. Tengs, A. Krasnov, S. J. Monaghan, M. Ballantyne, C. Penaloza, M. D. Fast, J. E. Bron, R. Houston, N. Robinson, D Robledo

“…Conclusions We chart the transcriptomic activity of subclusters of putative differentiating stromal cells during the process of wound healing for the first time, revealing different spatial niches of the various putative MSC subclusters, and setting the stage for further investigation of the manipulation of transitioning cell types to improve fish health.…”
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