scMalignantFinder distinguishes malignant cells in single-cell and spatial transcriptomics by leveraging cancer signatures by Qiaoni Yu, Yuan-Yuan Li, Yunqin Chen

“…Furthermore, scMalignantFinder holds the potential to annotate malignant regions in tumor spatial transcriptomics. Overall, we provide an efficient tool for detecting heterogeneous malignant cell populations.…”
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Transcriptome comparison revealed the difference in subcutaneous fat metabolism of Qinghai yak under different feeding conditions. by Weiqin Ding, Yonggang Sun, Yincang Han, Yaqian Liu, Shengwei Jin

“…KEGG revealed that the DEGs are mainly enriched for PPAR signaling pathway, AMPK signaling pathway and other pathways related to lipid metabolism. This study provides a scientific basis for further research on the effects of mRNA on subcutaneous fat in yaks under different feeding conditions.…”
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The relationship between deltamethrin-induced behavioral changes and acetylcholinesterase activity in zebrafish embryos or larvae based on transcriptome by Chunyu Liu, Yantong Guo, Xue Zhang, Hongsong Chen, Maomao Han, Han Wang, Jieyao Niu, Jinfei He, Jingfeng Yang, Wu Dong, Jiangdong Xue

“…It also caused a decrease in the expression of acetylcholinesterase-associated genes and the activity of acetylcholinesterase, which also led to an increase in the acetylcholinesterase content. The transcriptome data also showed that low concentration DM induced acetylcholine-related gene signaling pathways. …”
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Spatial transcriptomic profiling of the human fallopian tube epithelium reveals region-specific gene expression patterns by Jared Sipes, Sagar Rayamajhi, Leonidas E. Bantis, Rashna Madan, Amrita Mitra, Rajni V. Puri, Mohammod Mahmudur Rahman, Foyez Ahmmed, Harsh B. Pathak, Andrew K. Godwin

“…Despite its importance, the spatial transcriptome of the FT’s distinct anatomical regions (fimbria, infundibulum, ampulla, and isthmus) remains underexplored. …”
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Comparative transcriptomics analysis reveals stage-specific gene expression profiles associated with gamete formation in Garlic by Jie Ge, Jide Fan, Yongqiang Zhao, Xinjuan Lu, Canyu Liu, Biwei Zhang, Qingqing Yang, Mengqian Li, Yan Yang, Feng Yang

“…Taken together, these results provide insight into the molecular mechanisms and regulatory networks underlying gamete development in garlic and point to a set of candidate genes for further functional characterization.…”
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The important role of cuproptosis and cuproptosis-related genes in the development of thyroid carcinoma revealed by transcriptomic analysis and experiments by Yani Liu, Yanyan He, Shizhen Lei

“…For transcriptomic analysis, the transcriptomic data of THCA (n = 493) and normal thyroid samples (n = 58) was used. …”
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De novo transcriptome assembly of the Mediterranean sea-rock pool mosquitoes Aedes mariae and Aedes zammitii by Valentina Mastrantonio, Daniele Porretta, Franco Liberati, Roberta Bisconti, Tiziana Castrignanò, Daniele Canestrelli

“…These high-quality transcriptomes will provide valuable resources to investigate the role of hybridization in species adaptation to changing environments.…”
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Enhancing growth performance in Liangshan black sheep through fermented onion: insights from transcriptomics and metabolomics by Chaoyun Yang, Shuzhe Wang, Yunxia Qi, Yadong Jin, Ran Guan, Zengwen Huang

“…Rumen epithelial tissue was then collected for transcriptome sequencing, while fermented and unfermented onions were collected for untargeted metabolomics. …”
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De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens. by Yan-He Li, Han-Ping Wang, Hong Yao, Paul O'Bryant, Dean Rapp, Liang Guo, Eman A Waly

“…This study is the first report on transcriptome information in Percids, and provides rich resources for conducting further studies on understanding the molecular basis of sex determinations, sexual dimorphism, and sexual selection in fish, and for population studies and marker-assisted selection in Percids.…”
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De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes. by Jing Wu, Lanfen Wang, Long Li, Shumin Wang

“…The strategy for de novo assembly of transcriptome data generated here will be useful in other legume plant transcriptome studies. …”
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Comparison of the transcriptomes of mouse skin derived precursors (SKPs) and SKP-derived fibroblasts (SFBs) by RNA-Seq. by Yujie Mao, Lidan Xiong, Siyu Wang, Jianqiao Zhong, Rongying Zhou, Li Li

“…Here we compare the transcriptomes of mouse SKPs and SKP-derived fibroblasts (SFBs) by RNA-Seq analysis, trying to find differences in gene expression between the two kinds of cells and then elucidate the candidate genes that may play important roles in the differentiation of SKPs into fibroblasts. …”
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A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression. by Kory R Johnson, C C T Hindmarch, Yasmmyn D Salinas, YiJun Shi, Michael Greenwood, See Ziau Hoe, David Murphy, Harold Gainer

“…These data provide the research community a comprehensive view of the transcriptome in the SON under normosmotic conditions and the changes in specific gene expression evoked by salt loading.…”
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Spatial transcriptomics reveals tumor microenvironment heterogeneity in EBV positive diffuse large B cell lymphoma by Mei-yao He, Meng Liu, Jiayin Yuan, Jin Lv, Wei Li, Qianwen Yan, Yujiao Tang, Luyi Wang, Li Guo, Fang Liu

“…Here, we integrated 10X Visium spatial transcriptomics (ST) with single-cell RNA sequencing (scRNA-seq) to map TME heterogeneity in EBV+DLBCL. …”
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Comparative Transcriptome Analysis Reveals Effects of Exogenous Hematin on Anthocyanin Biosynthesis during Strawberry Fruit Ripening by Yi Li, Huayin Li, Fengde Wang, Jingjuan Li, Yihui Zhang, Liangju Wang, Jianwei Gao

“…In summary, exogenous hematin could promote fruit coloring by increasing anthocyanin content in the white stage of strawberries. Furthermore, transcriptome analysis suggests that hematin-promoted fruit coloring occurs through multiple related metabolic pathways, which provides valuable information for regulating fruit color via anthocyanin biosynthesis in strawberries.…”
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Integration of metabolic and transcriptomic analyses for revealing the galactose metabolism of tobacco (Nicotiana tabacum) under salt stress by Ge Bai, Ge Bai, Hui Zhang, Hui Zhang, Yong Li, Da-Hai Yang, Mingliang Fei, Tao Pang, Yaning Fu, Ai-Guo Yang, Zhen-Yu Wang, Jinbao Gu, He Xie

“…Understanding the metabolic and transcriptomic responses of tobacco plants to salt stress is crucial for developing such strategies.ResultsThis study identified 238 up-regulated and 122 down-regulated metabolites in tobacco plants under long-term salt stress. …”
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Transcriptomic and biochemical insights into key gene networks driving bulbil development of Pinellia ternata (Thunb.) Breit. by Xiwei Jia, Xijia Jiu, Yuan Liu, Chao Guo, Dong Liu, Xin Zhao, Honggang Chen, Tao Du

“…Based on physiological and biochemical reactions as well as transcriptome technology, this study determined the content of endogenous metabolites and related enzyme activities during the five growth stages of the bulbils, obtained the transcriptome information of all samples. …”
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Transcriptome and miRNA Reveal the Key Factor Regulating the Somatic Embryogenesis of <i>Camellia oleifera</i> by Qinqin Xing, Kailiang Wang, Henfu Yin, Chaochen Yang, Minyan Wang

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Identification and validation of five ferroptosis-related molecular signatures in keloids based on multiple transcriptome data analysis by Zhen Sun, Yonghong Qin, Xuanfen Zhang

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Transcriptome analysis reveals regulatory mechanism of methyl jasmonate-induced monoterpenoid biosynthesis in Mentha arvensis L. by Tingting Huang, Wenjin Men, Ariuntungalag Myanganbayar, Undarmaa Davaasambuu

“…However, L-menthol content decreased slightly by 7.90% under 5 mM MJ treatment. Transcriptome analysis identified 4,659 differentially expressed genes (DEGs) in MJ-treated leaves. …”
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First insight into metal binding proteins from the de novo transcriptome of acanthocephalan parasite Dentitruncus truttae by Sara Šariri, Irena Vardić Smrzlić, Tatjana Mijošek Pavin, Vlatka Filipović Marijić

“…Protein sequences that could not be described using the PFAM database were grouped into three clusters characterized by a high preference for binding zinc and copper. This study provides the first transcriptomic insights into D. truttae and its MBPs, contributing to future research of the molecular mechanisms underlying metal accumulation in acanthocephalans. …”
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