Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) vari... by Guangxia Duan, Chaoni Liang, Jundong Su, Yan Liang, Wanming Li, Jinbo Zhang, Yigong Zhang

“….), a diploid annual legume of the Fabaceae family, is one of the major pulse crops cultivated by farmers with limited resources. While previous studies have explored salt tolerance in chickpeas, this study provides a comprehensive multi-omics perspective. …”
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Integrated Analysis of the Transcriptome and Metabolome Reveals the Network Regulating Fruit Taste in Sponge Gourd (<i>Luffa cylindrica</i>) by Yaqian Chai, Wenjing Qiu, Zhikun Li, Luyao Gao, Wenqi Dong, Peng Zhang, Shengjun Zhou, Xin Wang, Yuqiang Zhu, Yuyan Sun

“…Similarly, the lysine, phenylalanine, and tryptophan contents were higher in GT than in BT (1.48-, 1.60-, and 1.38 times higher, respectively). Transcriptomic analysis of GT and BT fruits identified 1821 upregulated and 1185 downregulated differentially expressed genes (DEGs) in GT, while metabolomic analysis detected 25 upregulated differentially accumulated metabolites (DAMs) and 28 downregulated DAMs in GT. …”
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Single-cell RNA sequencing uncovers dynamic roadmap during chicken spermatogenesis by Haishan Guo, Jianing Liu, Mingzhen Xu, Tingqi Zhu, Shuangxing Liu, Pingquan Liu, Huayuan Liu, Shi Tang, Zhunan Li, Weiwei Jin, Donghua Li, Yadong Tian, Xiangtao Kang, Guirong Sun

“…By constructing a single-cell transcriptomic atlas, we identified ten somatic cell subtypes and four germ cell subtypes, thereby elucidating the dynamic changes in gene expression during spermatogenesis. …”
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The archaeal class Nitrososphaeria is a key component of the reproductive microbiome in sponges during gametogenesis by Marta Turon, Vasiliki Koutsouveli, María Conejero, Sergi Taboada, Aida Verdes, José María Lorente-Sorolla, Cristina Díez-Vives, Ana Riesgo

“…Supporting our hypothesis, we observed significant transcriptomic differences in G. macandrewii, mainly associated with the immune system, indicating potential changes in the sponge’s recognition system. …”
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Integrated Transcriptomic and Metabolomic Analysis Reveals Nitrogen-Mediated Delay of Premature Leaf Senescence in Red Raspberry Leaves by Qiang Huo, Feiyang Chang, Peng Jia, Ziqian Fu, Jiaqi Zhao, Yiwen Gao, Haoan Luan, Ying Wang, Qinglong Dong, Guohui Qi, Xuemei Zhang

“…Superoxide sismutase (SOD) and peroxidase (POD) activities in the middle and lower functional leaves of T150 were higher than in CK, while catalase (CAT) activity was lower. Transcriptomic analysis identified 4350 significantly differentially expressed genes, including 2062 upregulated and 2288 downregulated genes. …”
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Potential threat of environmental toxin palytoxin to cerebral nerves: A mechanism study in vitro and in vivo by Xue Zhang, Lei Huang, Yinliang Liu, Xuewen Li, Huanying Zhou, Kang Qin, Shuang Li, Shuyue Ren, Xuexia Jia, Zhixian Gao

“…Furthermore, pretreatment with JNK and p38 inhibitors significantly restored mitochondrial membrane potential, ATP content, and cell viability, while reducing the expression of pro-apoptotic genes in HT22 cells. …”
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Deciphering the regulatory mechanisms of potato cold-induced sweetening via integrated time-course transcriptome and metabolome analysis by Guangcan Cui, Tingting Zhou, Tingting Zhou, Zhongliang Liu, Ting Wang, Qingguo Wang, Tengfei Liu

“…RNA sequencing and quantitative real-time PCR were employed to analyze gene expression changes, while metabolomic profiling was conducted using UHPLC-MS/MS. …”
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Molecular evidence for the inverse comorbidity between central nervous system disorders and cancers detected by transcriptomic meta-analyses. by Kristina Ibáñez, César Boullosa, Rafael Tabarés-Seisdedos, Anaïs Baudot, Alfonso Valencia

“…Our analysis points to specific genes and pathways, the upregulation of which could increase the incidence of CNS disorders and simultaneously lower the risk of developing Cancer, while the downregulation of another set of genes and pathways could contribute to a decrease in the incidence of CNS disorders while increasing the Cancer risk. …”
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Placental whole transcriptome expression profile in patients with early-onset, late-onset preeclampsia and gestational diabetes mellitus by Zhuo Chen, Li Yang, Li Geng, Xinwen Zhang, Mingyu Du, Yonghu Sun, Lin Zhao, Bing Bai, Xiaohong Li

“…EO-PE was associated with reduced T cells and B cells, while LO-PE had increased plasmacytoid dendritic and CD56bright natural killer cells. …”
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Nitrogen Deprivation Drives Red Motile Cell Formation in <i>Haematococcus pluvialis</i>: Physiological and Transcriptomic Insights by Hailiang Xing, Na Zhou, Kai Liu, Xiaotian Yan, Wanxia Li, Xue Sun, Liuquan Zhang, Fengjie Liu, Nianjun Xu, Chaoyang Hu

“…A transcriptomic analysis revealed substantial alterations in gene expression in response to ND. …”
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Transcriptomic and Metabolomic Analysis Reveal the Effects of Light Quality on the Growth and Lipid Biosynthesis in <i>Chlorella pyrenoidosa</i> by Tingting Zhu, Ge Guan, Lele Huang, Lina Wen, Linxuan Li, Maozhi Ren

“…Blue light induces a shift in carbon flux from carbohydrate to protein, while red light transfers carbon flux from protein to lipid. …”
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Integration of epigenomic and transcriptomic profiling uncovers EZH2 target genes linked to cysteine metabolism in hepatocellular carcinoma by Jaehyun Lee, Chaelin You, Geunho Kwon, Junho Noh, Kyubin Lee, Kyunghwan Kim, Keunsoo Kang, Kyuho Kang

“…Tazemetostat treatment of HCC cells increased BHMT and CDO1 expression while reducing levels of ferroptosis markers FSP1, NFS1, and SLC7A11. …”
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Spatial transcriptomics of fetal membrane-Decidual interface reveals unique contributions by cell types in term and preterm births. by Lauren S Richardson, Mary Elise Severino, Rahul Chauhan, Weibin Zhang, Marian Kacerovsky, Suresh K Bhavnani, Ramkumar Menon

“…Cluster 2 genes were predominantly found in AECs in PPROM and PTB, while Cluster 4 contained AMC and CTC genes identified in term labor cases. …”
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Genetic insights into alcohol-associated liver disease: integrative transcriptome-wide analysis identifies novel susceptibility genes by Qianchang Wang, Zhe Wang, Minzhe Hu, Fangfeng Liu, Fangfeng Liu, Zhengjian Wang

“…BackgroundAlcohol-associated liver disease (ALD) is a chronic condition influenced by both genetic and environmental factors. While GWAS has identified ALD-related loci (PNPLA3, MBOAT7, TM6SF2), underlying genetic mechanisms and therapeutic targets remain unclear.MethodsThis study utilized the FinnGen R12 dataset (488,982 participants) and GTEx v8 eQTL data to perform a cross-tissue transcriptome-wide association study (TWAS) using UTMOST, with single-tissue validation via FUSION. …”
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Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species by Wallner, Adrian, Klonowska, Agnieszka, Guigard, Ludivine, King, Eoghan, Rimbault, Isabelle, Ngonkeu, Eddy, Nguyen, Phuong, Béna, Gilles, Moulin, Lionel

“…While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. …”
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Transcriptomic and metabolomic analysis reveals hepatic lipid metabolism disruption in Japanese quail under polystyrene microplastics exposure by Xinxin Zhang, Lingyang Jing, Xiaoqing Pei, Qingyu Zhang, Hongfeng Zhao

“…The results showed that 0.02 mg/kg and 0.4 mg/kg PS-MPs exposure caused increasing food and water intake with weight gain and liver lipid droplets accumulation while 8 mg/kg PS-MPs exposure induced decreasing food and water intake with weight loss. …”
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Transcriptome dataset to investigate the effect of deep seawater on the gene expression and functional compounds of leaves of Ligularia stenocephalaNCBI. by Dewi Komang Anggita, Bimpe Suliyat Azeez, Se-Jin Oh, Jong-Kuk Na

“…Due to the lack of the reference genome for read mapping, the three transcriptome data from this study were merged to generate a reference transcriptome. …”
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Integration of transcriptome and immunophenotyping data highlights differences in the pathogenetic kinetics of B cells across immune-mediated disease by Kazuhiko Yamamoto, Mineto Ota, Keishi Fujio, Yasuo Nagafuchi, Tomohisa Okamura, Saeko Yamada, Hirofumi Shoda, Takahiro Itamiya, Toshihiko Komai, Shinji Izuka, Kosuke Matsuki

“…Objective To elucidate crucial immune cell subsets and associated immunological pathways by stratifying patients with immune-mediated diseases (IMDs) using immunophenotyping and transcriptomic approaches.Methods We conducted flow cytometric and transcriptomic analyses in 23 immune cell subsets derived from 235 patients with six IMDs, using our database, utilizing our database, ImmuNexUT. …”
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Unraveling tissue-specific molecular mechanisms orchestrating arsenic response processes in Pteris vittata through transcriptomic analysis by Shujun Wei, Ryota Moriuchi, Christine Dwi A.P. Wiyono, Chihiro Inoue, Mei-Fang Chien

“…Within 24 h, As was translocated to fronds, while As concentration among fronds differed (4.08–1323.35 µg/g-DW). …”
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Transcriptomic and Metabolomic Exploration of the Therapeutic Effects of Prunus cerasifera Ehrh. Polyphenol on Metabolic-associated Fatty Liver Disease by Zaifu ZHOU, Yuxia WANG, Daohong CHEN, Hongbo REN, Quansong LIN

“…The effects of PCP on the liver transcriptome and serum bile acid metabolic profile of mice was also analyzed. …”
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