The Exon-Based Transcriptomic Analysis of Parkinson’s Disease by Sulev Kõks

“…Blood-based whole transcriptome analysis of the longitudinal PPMI cohort was performed with a focus on the change in the expression of exons to find potential RNA-based biomarkers. …”
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Dynamic transcriptome landscape of oat grain development by Ting Wang, Bing Han

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The light responsive transcriptome of the zebrafish: function and regulation. by Benjamin D Weger, Benjamin D Weger, Meltem Sahinbas, Georg W Otto, Philipp Mracek, Olivier Armant, Dirk Dolle, Kajori Lahiri, Daniela Vallone, Laurence Ettwiller, Robert Geisler, Nicholas S Foulkes, Thomas Dickmeis

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Metabolomic and transcriptomic stress response of Escherichia coli by Szymon Jozefczuk, Sebastian Klie, Gareth Catchpole, Jedrzej Szymanski, Alvaro Cuadros‐Inostroza, Dirk Steinhauser, Joachim Selbig, Lothar Willmitzer

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Blood transcriptomic associations of epigenetic age in adolescents by Dennis Khodasevich, Anne K Bozack, Saher Daredia, Julianna Deardorff, Kim G Harley, Brenda Eskenazi, Weihong Guo, Nina Holland, Andres Cardenas

“…Thirteen widely used epigenetic clocks were calculated, and their associations with transcriptome-wide RNA expression were tested using the limma-voom pipeline. …”
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TauL1, TauL2 and TauL3 gene-pools of Aegilops tauschii essentially differ in their genetic expression patterns by Alexander Ju. Dudnikov, Gennady V. Vasiliev, Ming Hao, Deng-Cai Liu, Fan Xing, Mehdi Mansouri, Dmitry A. Afonnikov, Nikolay A. Shmakov

“…Aegilops tauschii is a wild diploid goat-grass which occupies a vast range in Central Eurasia and comprises three different gene-pools: TauL1, TauL2, and TauL3. Multivariate statistical analysis of the transcriptomes from the leaf tissue of 40 A. tauschii accessions, 18 of TauL1, 20 of TauL2, and 2 of TauL3, revealed that the gene-pools of A. tauschii distinctly and essentially differ in their genetic expression patterns. …”
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Interaction between the liver transcriptome and gut microbiota in mice during Toxoplasma gondii infection as identified by integrated transcriptomic and microbiome analysis by Yang Zou, He Ma, Xing Yang, Xin-Yu Wei, Chao Chen, Jing Jiang, Tao Jiang

“…Then, we performed fecal 16S rRNA gene amplicon sequencing and RNA transcriptome sequencing to investigate the composition of the gut microbiota and the expression profiles of long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) in the livers of mice infected with T. gondii at different stages of infection. …”
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Single-cell transcriptomic characterization of microscopic colitis by Stefan Halvorsen, Molly Thomas, Mari Mino-Kenudson, Yuko Kinowaki, Kristin E. Burke, David Morgan, Kaia C. Miller, Katherine M. Williams, Jenny Gurung, Jessica McGoldrick, Megan Hopton, Brooke Hoppe, Nandini Samanta, Sidney Martin, Alice Tirard, Benjamin Y. Arnold, Jessica Tantivit, Joseph Yarze, Kyle Staller, Daniel C. Chung, Alexandra-Chloé Villani, Slim Sassi, Hamed Khalili

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Single-Cell Transcriptomic Analysis of Kaposi Sarcoma. by Daniel A Rauch, Paula Valiño Ramos, Mariam Khanfar, John Harding, Ancy Joseph, Anam Fahad, Paul Simonson, Isabel Risch, Obi Griffith, Malachi Griffith, Lee Ratner

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Current status of transcriptome sequencing technology in ruminants by Cui JiaYu, Song Lili, Wang Dawei, Liu ZhiLin, Zhang Xin, Jia Zelin, Zhang Yuhang, Xiong Huisheng, Wang Xueli

“…Transcriptome sequencing can detect genes with low expression levels, identify new gene transcripts and alternative splicing events, detect and analyze the biological regulatory mechanisms of the body, reveal differences in gene expression levels during breeding, and reveal the interaction between hosts and pathogens. …”
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Multi-omics analysis identified macrophages as key contributors to sex-related differences in ulcerative colitis by Xiaojie Fang, Jiahao Yang, Liu Yang, Yiyou Lin, Yanyan Li, Xin Yin, Xiaobing Dou, Chenyun Miao

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Transcriptome dataset of leaves treated with different spectra of light-emitting diodes on Sandoricum koetjape Merr. seedlings using cDNA-PCR sequencing with Oxford nanopore technologiesMendeley Data by Asyhuriyah Wardah Defitrianida, M. Adrian, Pandi Ariansah, Roedhy Poerwanto, Eiichi Inoue, Dhika Prita Hapsari, Deden Derajat Matra

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Intracellular spatial transcriptomic analysis toolkit (InSTAnT) by Anurendra Kumar, Alex W. Schrader, Bhavay Aggarwal, Ali Ebrahimpour Boroojeny, Marisa Asadian, JuYeon Lee, You Jin Song, Sihai Dave Zhao, Hee-Sun Han, Saurabh Sinha

“…We showcase the toolkit on five different datasets representing two different cell lines, two brain structures, two species, and three different technologies. …”
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Metabolome and transcriptome of Fu tea fermented by Aspergillus montevidensis by LI Jianmiao, DING Xiaowei, ZHANG Lixu, MA Xueni

“…In order to investigate the effect of Aspergillus montevidensis on the quality of Fu tea, the dark tea was fermented by inoculation with A. montevidensis, the metabolites in tea soup with different fermentation time was analyzed by ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS), and the metabolome and transcriptome analysis were performed based on the results. …”
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Dissection of transcriptome and metabolome insights into the polyphyllin biosynthesis in Paris by Ping Xu, Qi Mi, Xiaoye Zhang, Xuan Zhang, Mengwen Yu, Yingsi Gao, Xiheng Wan, Yichun Chen, Qiaoyuan Li, Jia Chen, Guowei Zheng

“…Abstract Background Polyphyllins are significant medicinal compounds found in Paris species, with different polyphyllins fulfilling distinct medicinal roles. …”
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Integrating physiological and transcriptomic analyses at the single-neuron level by Haruya Yagishita, Takuya Sasaki

“…Neurons generate various spike patterns to execute different functions. Understanding how these physiological neuronal spike patterns are related to their molecular characteristics is a long-standing issue in neuroscience. …”
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Full transcriptome analysis of early dorsoventral patterning in zebrafish. by Erika Fodor, Áron Zsigmond, Balázs Horváth, János Molnár, István Nagy, Gábor Tóth, Stephen W Wilson, Máté Varga

“…A combination of different statistical approaches yielded 41 differentially expressed candidate genes and we confirmed by in situ hybridization the early dorsal expression of 32 genes that are transcribed shortly after the onset of zygotic transcription. …”
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Network architecture of transcriptomic stress responses in zebrafish embryos. by Kaylee Beine, Lauric Feugere, Alexander P Turner, Katharina C Wollenberg Valero

“…Across treatments, differentially expressed genes in different parts of the network affected identical phenotypes. …”
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Comparative transcriptomics of pathogenic and non‐pathogenic Listeria species by Omri Wurtzel, Nina Sesto, J R Mellin, Iris Karunker, Sarit Edelheit, Christophe Bécavin, Cristel Archambaud, Pascale Cossart, Rotem Sorek

“…We used strand‐specific cDNA sequencing to produce genome‐wide transcription start site maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. …”
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Comprehensive transcriptome of muscle development in Sichuan white rabbit by Xiangyu Zhang, Kai Zhang, Dengping Huang, Shangjun Yang, Min Zhang, Qin Yin

“…Results We generated extensive transcriptome datasets (mRNAs, miRNAs and lncRNAs) revealing the myogenic regulatory network at different time points. …”
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