Comprehensive evaluation of methods for identifying tissues or cell types of origin of the plasma cell-free transcriptome by Tingyu Yang, Yulong Qin, Shuo Yan, Sijia Guo, Jinghua Sun, Jiayi Huang, Jiayi Li, Qing Zhou, Xin Jin, Wen-Jing Wang

“…In this study, we employed human tissue and cell transcriptomic data as reference sets and evaluated the performance of seven deconvolution methods on cfRNA. …”
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Integrating metabolomics and transcriptomics to analyze differences in muscle mass and flavor formation in Gayal and yellow cattle by Lin Han, Lin Han, Runqi Fu, Runqi Fu, Binlong Fu, Binlong Fu, Qian Li, Qian Li, Ye Yu, Ye Yu, Huan Gao, Huan Gao, Jiawei Zhang, Min Qi, Min Qi, Chunjia Jin, Chunjia Jin, Shengyong Mao, Jing Leng, Jing Leng

“…Beef flavor is affected by muscle metabolites and their related regulatory genes, and the molecular regulatory mechanisms vary among different beef breeds. To provide some new ways to improve meat quality and cattle breed improvement, 24-month-old Gayal (n = 8) and yellow cattle (n = 8) were selected for comparison in this study. …”
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Characterization of chemosensory genes in the subterranean pest Gryllotalpa Orientalis based on genome assembly and transcriptome comparison by Amna Chudhary, De-Long Guan, Yandi Xu, Tao Jiang, Lulu Yang, Mengyang Chen, Muhammad Salabat Khan, Wenhui Zhu, Sheng-Quan Xu

“…These findings provide a basis for future functional studies and highlight the role of chemoreception in the subterranean environment.…”
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Integrated genome and transcriptome analysis reveals pathogenic mechanisms of Calonectria eucalypti in Eucalyptus leaf blight by QianLi Liu, GuoQing Li, YuHua Liang, Yan Lin, KaiDong Liu, ZhenChi Huang, ShanNi Cao, FeiFei Liu

“…Conclusions This study provides the first integrative genome and infection-stage transcriptome map of C. eucalypti, revealing a coordinated, stage-specific deployment of pathogenicity-related gene clusters. …”
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Time-course transcriptomic information reveals the mechanisms of improved drought tolerance by drought priming in wheat by Qing Li, Zhuangzhuang Sun, Zihan Jing, Xiao Wang, Chuan Zhong, Wenliang Wan, Maguje Masa Malko, Linfeng Xu, Zhaofeng Li, Qin Zhou, Jian Cai, Yingxin Zhong, Mei Huang, Dong Jiang

“…These findings provide new insights into the physiological and molecular mechanisms of the long-term effects of early drought priming that can effectively improve drought tolerance in wheat, and may provide potential approaches for addressing the challenges of increasing abiotic stresses and securing food safety under global warming scenarios.…”
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Transcriptome analysis reveals the common and specific pathways of citric acid accumulation in different citrus species by Jiaxian He, Juan Sun, Yue Huang, Lun Wang, Shengjun Liu, Zhenghua Jiang, Xia Wang, Qiang Xu

“…Overall, this study provides an insight into the mechanism of citric acid accumulation in citrus fruit and provides useful references for fruit quality improvement through acidity control in different citrus species.…”
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MuCST: restoring and integrating heterogeneous morphology images and spatial transcriptomics data with contrastive learning by Yu Wang, Zaiyi Liu, Xiaoke Ma

“…Abstract Spatially resolved transcriptomics (SRT) simultaneously measure spatial location, histology images, and transcriptional profiles of cells or regions in undissociated tissues. …”
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Single-Cell Sequencing Combined with Transcriptome Sequencing to Explore the Molecular Mechanisms Related to Skin Photoaging by Hu X, Du S, Chen M, Yang H, He J, Zhang L, Tan B, Wu T, Duan X

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Integration of transcriptomic and metabolomic analysis reveals light-regulated anthocyanin accumulation in the peel of ‘Yinhongli’ plum by Bo Xiong, Yisong Li, Junfei Yao, Jialu Wang, Linlyu Han, Qingqing Ma, Taimei Deng, Ling Liao, Lijun Deng, Guochao Sun, Mingfei Zhang, Xun Wan, Siya He, Jiaxian He, Zhihui Wang

“…Transcriptomic profiling revealed 6,900 differentially expressed genes (DEGs) between YD and YL, demonstrating significant correlations between the phenylpropanoid and flavonoid biosynthetic pathways. …”
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An integrative analysis of cell-specific transcriptomics and nuclear proteomics of sleep-deprived mouse cerebral cortex by Pawan K. Jha, Utham K. Valekunja, Akhilesh B. Reddy

“…By combining cell-type specific transcriptomics and nuclear proteomics we investigated how sleep loss affects the cellular composition and molecular profiles of these two cell types in a focused approach. …”
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Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. by Kristine B Arnvig, Iñaki Comas, Nicholas R Thomson, Joanna Houghton, Helena I Boshoff, Nicholas J Croucher, Graham Rose, Timothy T Perkins, Julian Parkhill, Gordon Dougan, Douglas B Young

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Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset by Tracy Chew, Tiana M. Pelaia, Amy L. Phu, Sally Teoh, Ya Wang, Nandan Deshpande, Karan Kim, Velma Herwanto, Gunawan, Thomas Karvunidis, Yoann Zerbib, Kirsty R. Short, Stephen Macdonald, Irani Thevarajan, Darawan Rinchai, Win Sen Kuan, Ben Knippenberg, Jonathan Iredell, Philip N. Britton, Owen Hutchings, Warwick J. Britton, John-Sebastian Eden, Sam Orde, Benjamin Tang, Anthony McLean, Damien Chaussabel, Klaus Schughart, Maryam Shojaei

“…Understanding the molecular mechanisms underlying the pathogenicity of these infections is crucial for developing effective interventions. RNA sequencing provides insights into a patient’s global transcriptome changes, facilitating the identification of host gene signatures in response to infection and potential therapeutic targets. …”
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Genomic and transcriptomic landscapes of metastatic neuroendocrine neoplasms from distinct primary sites and their clinical implications by Kathleen Wee, Kevin C. Yang, David F. Schaeffer, Chen Zhou, Emily Leung, Xiaolan Feng, Janessa Laskin, Marco A. Marra, Jonathan M. Loree, Sharon M. Gorski

“…Comparison to several reference transcriptome data sets revealed that despite considerable whole genome and transcriptome variability in NENs, the metastatic NENs are still more like each other than other cancer types. …”
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Transcriptomic and targeted metabolomic analysis identifies genes involved in differential anthocyanin accumulation in potato tubers by Rui Yang, Shuohan Huang, Dan Li, Yuan Sun, Guangdong Zhou, Duanrong Zhou, Binquan Huang

“…To identify genes and metabolites involved in anthocyanin accumulation, we performed comparative transcriptomic and metabolomic analyses of pith and vasculature tissues from the tubers of three different potato cultivars. …”
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Left atrial single-cell transcriptomics reveals amphiregulin as a surrogate marker for atrial fibrillation by Yuya Suzuki, Takuo Emoto, Shunsuke Sato, Takeshi Yoshida, Mitsuhiko Shoda, Hiromi Endoh, Manabu Nagao, Tomoyo Hamana, Taishi Inoue, Tomohiro Hayashi, Eriko Nitta, Hiroki Konishi, Kunihiko Kiuchi, Mitsuru Takami, Kimitake Imamura, Masayuki Taniguchi, Masatoshi Inoue, Toshihiro Nakamura, Yusuke Sonoda, Hiroyuki Takahara, Kazutaka Nakasone, Kyoko Yamamoto, Kenichi Tani, Hidehiro Iwai, Yusuke Nakanishi, Shogo Yonehara, Atsushi Murakami, Ryuji Toh, Takenao Ohkawa, Tomoyuki Furuyashiki, Ryo Nitta, Tomoya Yamashita, Ken-ichi Hirata, Koji Fukuzawa

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Phenotypic, transcriptomic and metabolomic changes in Klebsiella pneumoniae after long term exposure to simulated microgravity by Xia Wang, Zili Chai, Wenting Liu, Tianye Jia, Zilong Yang, Fengwei Zhang, Fuqiang Kang, Qiming Wang, Xianwei Ye, Hongguang Ren, Xiaodong Zai, Junjie Yue, Yuan Jin

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Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implications by Xiaoxiao Wang, David Venet, Frédéric Lifrange, Denis Larsimont, Mattia Rediti, Linnea Stenbeck, Floriane Dupont, Ghizlane Rouas, Andrea Joaquin Garcia, Ligia Craciun, Laurence Buisseret, Michail Ignatiadis, Marcela Carausu, Nayanika Bhalla, Yuvarani Masarapu, Eva Gracia Villacampa, Lovisa Franzén, Sami Saarenpää, Linda Kvastad, Kim Thrane, Joakim Lundeberg, Françoise Rothé, Christos Sotiriou

“…Abstract While triple-negative breast cancer (TNBC) is known to be heterogeneous at the genomic and transcriptomic levels, spatial information on tumor organization and cell composition is still lacking. …”
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De novo assembly of transcriptome during regeneration post-arm amputation in the starfish, Asterias amurensis by Mi Jeong Jo, Hye-Jin Go, Jeong Gyu Kim, Gun-Do Kim

“…Abstract Objectives This study investigates the nerve cord transcriptome of Asterias amurensis to explore its regenerative abilities. …”
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Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts. by Junpeng Gao, Yuxuan Zheng, Lin Li, Minjie Lu, Xiangjian Chen, Yu Wang, Yanna Li, Xiaomeng Liu, Yun Gao, Yunuo Mao, Peng Zhao, Jinan Zhang, Fuchou Tang, Lei Song, Lu Wen, Jizheng Wang

“…Our results showed conserved region-specific patterns in the mammalian heart at transcriptome and DNA methylation level. Adult and fetal human hearts showed distinct features in DNA methylome, chromatin accessibility, and transcriptome. …”
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Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development by Qingyuan Zhu, Ying Liu, Xin Hao, Shengyi Yan, Jitao Ge, Changqing Zheng, Xianwen Ren, Fan Zhou

“…The epigenome dynamics such as DNA methylome and transcriptome of embryos have been analyzed, while the coordination between these two molecular layers controlling lineage fate remained elusive. …”
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