Multiscale Dissection of Spatial Heterogeneity by Integrating Multi‐Slice Spatial and Single‐Cell Transcriptomics by Yuqi Chen, Caiwei Zhen, Yuanyuan Mo, Juan Liu, Lihua Zhang

“…Existing methods for analyzing spatially resolved transcriptomics (SRT) are separately designed for either domain alignment across multiple slices or deconvoluting cell type compositions within a single slice. …”
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Fibrolamellar carcinoma transcriptomic-based treatment prediction: complete response after nivolumab and ipilimumab by Razelle Kurzrock, Eytan Ruppin, Raanan Berger, Gal Dinstag, Omer Tirosh, Eyal Schiff, David Kleiner, Kenneth D Aldape, Tuvik Beker

“…Here, combined checkpoint blockade guided by novel transcriptomic analysis led to complete remission after failure of several lines of treatment.…”
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Genomic, transcriptomic and epigenomic signatures of ageing and cold adaptation in the Antarctic clam Laternula elliptica by Victoria A. Sleight, Melody S. Clark, Meghan K. Yap-Chiongco, Frances Turner, Kevin M. Kocot

“…In this study, we describe and analyse the genome of L. elliptica and use it as a tool to understand transcriptomic responses to shell damage across different age cohorts. …”
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ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets by Zhaorong Li, Juan I. Fuxman Bass, Juan I. Fuxman Bass, Juan I. Fuxman Bass, Juan I. Fuxman Bass

“…To test the performance of ICARus, we analyzed transcriptome datasets obtained from COVID-19 patients with different outcomes and from lung adenocarcinoma. …”
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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

“…Approximately 64.63 million reads from Illumina Novaseq 6000 were generated from three different ovarian stages tissue assembled in Trinity assembler. …”
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Host plant driven transcriptome plasticity in the salivary glands of the cabbage looper (Trichoplusia ni). by Loren J Rivera-Vega, David A Galbraith, Christina M Grozinger, Gary W Felton

“…Feeding on different host plant diets resulted in substantial remodeling of the gland transcriptomes, with 4,501 transcripts significantly differentially expressed across the three treatment groups. …”
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Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G‐protein action by Sona Pandey, Rui‐Sheng Wang, Liza Wilson, Song Li, Zhixin Zhao, Timothy E Gookin, Sarah M Assmann, Réka Albert

“…Conversely, some theoretical regulatory modes of the G‐protein are not supported; (2) a new mechanism of G‐protein signaling is revealed, in which Gβ regulates gene expression identically in the presence or absence of Gα; (3) guard cells and leaves favor different G‐protein modes in transcriptome regulation, supporting system specificity of G‐protein signaling. …”
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A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus. by Bethany A Stahl, Joshua B Gross, Daniel I Speiser, Todd H Oakley, Nipam H Patel, Douglas B Gould, Meredith E Protas

“…Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. …”
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Transcriptome profiling of intrahepatocytic Plasmodium and their host hepatocytes based on the infection phase and the zonation of the liver by Zhuning Mo, Zhuning Mo, Yuhong Chen, Yuhong Chen, Yujuan Qin, Yujuan Qin, Jian Song, Jian Song, Jian Song

“…A joint investigation of the Plasmodium transcriptome and their host transcriptome was carried out to confer a comprehensive analysis of gene expression in the liver stage of Plasmodium infection in vivo, which is similar to the disease setting, and therefore deepen our understanding of parasite and host transcriptional dynamics during intrahepatocytic infection.…”
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Evolutionary analysis of novel serine proteases in the venom gland transcriptome of Bitis gabonica rhinoceros. by Sakthivel Vaiyapuri, Simon C Wagstaff, Robert A Harrison, Jonathan M Gibbins, E Gail Hutchinson

“…<h4>Methodology and principal findings</h4>Four serine protease-encoding genes from the venom gland transcriptome of Bitis gabonica rhinoceros were amplified and sequenced. …”
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Metagenomic and Transcriptomic Datasets of Plateau Brown Frogs (Rana kukunoris) from the Helan Mountains by Nan Zhang, Yao Zhao, Zhirong Zhang, Meiling Zhan, Xuyang Zhao, Yi Zhang, Jingyu Sun, Yuxuan Zhang, Liwei Teng, Zhensheng Liu

“…Therefore, this study investigates the adaptation strategies of the plateau brown frog to environmental changes, providing extensive transcriptomic and the first comprehensive metagenomic dataset from two distinctly different environmental regions (eastern and western slopes of the Helan Mountains). …”
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Unique intrahepatic transcriptomics profiles discriminate the clinical phases of a chronic HBV infection. by Jun Hou, Willem P Brouwer, Kim Kreefft, Lucio Gama, Sarah L Price, Harry L A Janssen, Pim J French, Thomas Vanwolleghem, Andre Boonstra

“…We performed an in-depth transcriptome analysis of archived FFPE liver biopsies of each clinical phase to address host determinants associated with the natural history. …”
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Transcriptome Analysis Reveals Key Pathways and Genes Involved in Lodging Resistance of Upland Cotton by Yuan Wang, Ao Feng, Caiwang Zhao, Xiaomei Ma, Xinyu Zhang, Yanjun Li, Jie Sun

“…In this study, the morphological and physiological characteristics and transcriptome of two upland cotton varieties with different lodging resistance were compared. …”
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Transcriptome of Taenia solium during in vitro cyst activation and initial growth into the tapeworm stage by David Castaneda-Carpio, Renzo Gutierrez-Loli, Jose Maravi-Jaime, Segundo W. Del Aguila, Valeria Villar-Davila, Luz M. Moyano, Rafael Tapia-Limonchi, Stella M. Chenet, Cristina Guerra-Giraldez

“…We present a transcriptome generated by Next Generation Sequencing from T. solium cysts activated in culture and collected at three different in vitro growth phases, defined by their morphology. …”
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Comparative transcriptome analysis reveals pathogenesis of Procambarus clarkii during Black May Disease by Xueqi Teng, Chengwen Song, Yuxin Fan, Shiyu Jin, Si Luo

“…To better understand the progression of BMD, this study integrates key hepatopancreatic enzyme activity data with intestinal transcriptome profiles. We systematically investigated the immune, antioxidant, and metabolic adaptations of P. clarkii across different stages of the disease from both functional and molecular perspectives. …”
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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

“…Thus, the differentially expressed genes among the different tissues and sexes lays a good foundation for the olfaction researches in T. absoluta. …”
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Exploring the mechanism of seed shattering in Psathyrostachys juncea through histological analysis and comparative transcriptomics by Yuru Lv, Lan Yun, Miaomiao Jia, Yixin Mu, Zhiqiang Zhang

“…The degradation of the AZ in H occurred earlier and was more severe compared to L. At different developmental stages of the AZ, H exhibited higher cellulase and polygalacturonase activities and higher abscisic acid contents compared to L. …”
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Transcriptomic network underlying physiological alterations in the stem of Myricaria laxiflora in response to waterlogging stress by Linbao Li, Yang Su, Weibo Xiang, Guiyun Huang, Qianyan Liang, Bicheng Dun, Haibo Zhang, Zhiqiang Xiao, Liwen Qiu, Jun Zhang, Di Wu

“…The principal component analysis (PCA) of transcriptomes from five different timepoints uncovered PC1 counted for 17.3 % of total variations and separated the treated and non-treated samples. …”
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Mining key genes of alkaloid synthesis pathway in lotus leaves based on metabolomics and transcriptomics by LI Shuangqin, WANG Zhongyi, ZHAO Wanyue, CHEN Longqing, HU Huizhen

“…In order to explore the molecular mechanism of alkaloid biosynthesis in lotus leaves, metabolomics and transcriptomics sequencing analyses were performed on mature lotus leaves of ‘Taikong Lian’ (high alkaloid content), ‘Juwuba’ (medium alkaloid content) and ‘Dazu Honglian’ (low alkaloid content) cultivars with significant differences in alkaloid content. …”
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A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics by Amitabh C. Pandey, Jon Bezney, Dante DeAscanis, Ethan B. Kirsch, Farin Ahmed, Austin Crinklaw, Kumari Sonal Choudhary, Tony Mandala, Jeffrey Deason, Jasmin S. Hamidi, Azeem Siddique, Sridhar Ranganathan, Keith Brown, Jon Armstrong, Steven Head, Phillip Ordoukhanian, Lars M. Steinmetz, Eric J. Topol

“…We experimentally apply scCLEAN to both heterogeneous immune cells and homogenous vascular smooth muscle cells to demonstrate its ability to uncover biological signatures in different biological contexts. We further emphasize scCLEAN’s versatility by applying it to a third-generation sequencing method, single-cell MAS-Seq, to increase transcript-level detection and discovery. …”
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