Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq by Chunyao Wei, Jeannie T. Lee

“…Summary: Strand-optimized Smart-seq (So-Smart-seq) can capture a comprehensive transcriptome from low-input samples. This technique detects both polyadenylated and non-polyadenylated RNAs, inclusive of repetitive RNAs, while excluding highly abundant ribosomal RNAs. …”
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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

“…Transcriptome analysis identified 8,386 differentially expressed genes, with enriched pathways in hormone signaling, photosynthesis, and amino acid metabolism. …”
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XModNN: Explainable Modular Neural Network to Identify Clinical Parameters and Disease Biomarkers in Transcriptomic Datasets by Jan Oldenburg, Jonas Wagner, Sascha Troschke-Meurer, Jessica Plietz, Lars Kaderali, Henry Völzke, Matthias Nauck, Georg Homuth, Uwe Völker, Stefan Simm

“…The integrated pathway relevance analysis improves a standard gene set overrepresentation analysis, which relies solely on gene assignment. …”
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De-novo transcriptome sequencing of a normalized cDNA pool from influenza infected ferrets. by Jeremy V Camp, Thomas L Svensson, Alexis McBrayer, Colleen B Jonsson, Peter Liljeström, Carl E Bruder

“…The majority of genes involved in innate or adaptive immune response are still lacking, restricting molecular genetic analysis of host response in the ferret model. To enable de novo identification of transcriptionally active ferret genes in response to infection, we performed de-novo transcriptome sequencing of animals infected with H1N1 A/California/07/2009. …”
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Transcriptome sequencing revealed the regulation of stem internode length associated with mechanical harvesting in three tea varieties by Xiaozeng Mi, Xiaozeng Mi, Dahe Qiao, Dahe Qiao, Chun Yang, Chun Yang, Juan Chen, Sihui Liang, Sihui Liang, Yan Guo, Yan Guo

“…GO, KEGG enrichment and WGCNA were used to identify key genes, and their expression levels in three tea tree varieties were validated by qRT-PCR.ResultIn this study, we measured the internode lengths of the three varieties and found that their internode lengths were ‘Feiyun’ > ‘Qiancha 1’ > ‘Longjing 43’. 10,518 differentially expressed genes were identified through transcriptome sequencing and analysis. GO and KEGG enrichment showed that these differentially expressed genes were mainly enriched in plant hormone signal transduction and DNA-binding transcription factor activity pathways. …”
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A global overview of transcriptome dynamics during the late stage of flower bud development in Camellia oleifera by Huiyun Song, Zhihao Duan, Heqiang Huo, Xiaoling Wang, Yujuan Wang, Junhui Chen, Liang Jin, Mengfei Lin

“…The study investigated the dynamic changes and regulatory patterns of different tissues within flower buds from flower bud development to flowering, employing a multi-faceted approach that included cellular dissection, analysis of hormone content, and transcriptome analysis. …”
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Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds by Lijun Pan, Yifan Chen, Zeyu Ren, Dalia Mohamedkheir Khojely, Dalia Mohamedkheir Khojely, Siyu Wang, Yueming Li, Seifeldin Elrayah Ibrahim, Seifeldin Elrayah Ibrahim, Sujie Fan, Yang Song, Zhuo Zhang, Jian Wei

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Transcriptomic signatures of WNT-driven pathways and granulosa cell-oocyte interactions during primordial follicle activation. by Hinako M Takase, Tappei Mishina, Tetsutaro Hayashi, Mika Yoshimura, Mariko Kuse, Itoshi Nikaido, Tomoya S Kitajima

“…Our data revealed immediate transcriptomic changes in GCs post-PFA in Wls cKO mice, leading to a divergent trajectory, while oocytes exhibited modest transcriptomic alterations. …”
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Biomarkers associated with cell-in-cell structure in kidney renal clear cell carcinoma based on transcriptome sequencing by Zehua Wang, Zhongxiao Zhang

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Immuno-oncologic profiling by stage-dependent transcriptome and proteome analyses of spontaneously regressing canine cutaneous histiocytoma by Alina K. Loriani Fard, Alexander Haake, Vladimir Jovanovic, Sandro Andreotti, Michael Hummel, Benjamin-Florian Hempel, Achim D. Gruber

“…QuantSeq 3′ mRNA sequencing with functional over-representation analysis and an nCounter RNA hybridization assay were employed on 21 formalin-fixed, paraffin-embedded CCH samples representing three different tumor stages (dataset information: GSE261387—Immuno-Oncologic Profiling by Stage-Dependent Transcriptome and Proteome Analyses of Spontaneously Regressing Canine Cutaneous Histiocytoma—OmicsDI). …”
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Transcriptome and translatome profiling of Col-0 and grp7grp8 under ABA treatment in Arabidopsis by Jing Zhang, Yongxin Xu, Jun Xiao

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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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Transcriptomic and network toxicology approaches reveal potential mechanisms of DEHP induced intrahepatic cholestasis during pregnancy by Lun Zhang, Qianqian Huang, Yun Yu, Yue Jiang, Mengzhen Hou, Wenkang Tao, Cheng Zhang, Jianqing Wang

“…In conclusion, this study offers novel insights into the molecular mechanisms of DEHP-induced hepatotoxicity during pregnancy while providing a systematic framework for assessing risks associated with DEHP exposure; thus contributing to the prevention and treatment of ICP.…”
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Integrating transcriptomic and metabolomic analyses to characterize the potential function of SLC1A5 in thyroid cancer by Fengling Shan, Lan Wang, Xinyu Lu, Meihong Zhou, Zi Wang, Jingjing Lou, Xingdang Liu

“…SLC1A5 expression in TPC-1 and B-CPAP was knocked down using SLC1A5 siRNA to investigate its effects on cell growth and apoptosis. Transcriptome sequencing and metabolite analysis were carried out in the SLC1A5 siRNA group to identify major transcriptomic or metabolite changes that could lead to apoptosis. …”
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Varied cellular abnormalities in thin vs. normal endometrium in recurrent implantation failure by single-cell transcriptomics by Xiaoying Fu, Xiaoyan Guo, Han Xu, Yini Li, Bihui Jin, Xirong Zhang, Chongyi Shu, Yuhang Fan, Yiqi Yu, Yuqing Tian, Jiao Tian, Jing Shu

“…Results Through comparative analysis of differentially expressed genes among these groups and KEGG pathway analysis, the TE-RIF group exhibited notable dysregulations in the TNF and MAPK signaling pathways, which are pivotal in stromal cell growth and endometrial receptivity. …”
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The mechanism underlying B-cell developmental dysfunction in Kawasaki disease based on single-cell transcriptomic sequencing by Qiuping Lin, Zhen Wang, Guohui Ding, Guang Li, Liqin Chen, Qingzhu Qiu, Sirui Song, Wei Liu, Xunwei Jiang, Min Huang, Min Huang, Libing Shen, Tingting Xiao, Lijian Xie, Lijian Xie, Lijian Xie

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Effects of Geraniol on Survival, Reproduction, Endophytes, and Transcriptome of Tea Green Leafhoppers (<i>Empoasca onukii</i>) by Junjie Tian, Hainuo Hong, Shiliang Mo, Shiqin Mo, Hongliang Shi, Juan Shi, Ying Zhou

“…In order to investigate whether the release of geraniol is a defensive mechanism of tea plants against infestation by tea green leafhoppers, our study explored the effects of geraniol on tea green leafhoppers, including the selectivity of tea green leafhoppers’ response to geraniol, survival and reproductive parameters, as well as alterations in endophytes and the transcriptome. The findings indicated that while geraniol did not exhibit strong repellent or lethal effects on tea green leafhoppers, it significantly reduced the egg-laying and hatching rates. …”
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Muscle Spatial Transcriptomic Reveals Heterogeneous Profiles in Juvenile Dermatomyositis and Persistence of Abnormal Signature After Remission by Margot Tragin, Séverine A. Degrelle, Baptiste Periou, Brigitte Bader-Meunier, Christine Barnerias, Christine Bodemer, Isabelle Desguerre, Mathieu Paul Rodero, François Jérôme Authier, Cyril Gitiaux

“…The “myofibrillar stress signature” was prominent in the most severe biopsy while the “muscle remodeling” signature was mostly present in the biopsy from the patient with good outcome. …”
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Blood-based transcriptomic biomarkers for response to [177Lu]Lu-DOTA-TATE therapy in neuroendocrine tumors by Hyunpil Sung, Sungwoo Bae, Minseok Suh, Hongyoon Choi, Hyung-Jun Im, Gi Jeong Cheon, Keon Wook Kang

“…Abstract Background [177Lu]Lu-DOTA-TATE is an effective treatment for metastatic neuroendocrine tumors (NETs) expressing somatostatin receptors. While the tumor uptake [177Lu]Lu-DOTA-TATE of has shown potential as a predictive biomarker, patient response to the treatment varies significantly. …”
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Integration of GWAS and transcriptomic analyses reveal candidate genes for duck gonadal development during puberty onset by Mengru Xu, Qian Tang, Jingjing Qi, Xu Han, Qiuyu Tao, Yinjuan Lu, Yuan Bai, Shenqiang Hu, Liang Li, Lili Bai, Jiwei Hu, Jiwen Wang, Hehe Liu

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