Integrative Network Pharmacology and Transcriptomics Reveal the Mechanism of Gui-Qi-Yi-Shen Granules in the Treatment of IgA Nephropathy by Cao JW, Tang YW, Jiang MY, Lu MD, Yang RC, Yu DR, Wan F

“…Network pharmacology and transcriptomic analyses were performed to investigate the potential mechanisms of GQYS, while Western blotting and IF were performed to confirm these actions.Results: Compared to the model group, 24 h proteinuria and alanine aminotransferase levels were significantly reduced in the GQYS groups. …”
Get full text

Comparative transcriptomics of two petal variants reveals key functional genes underlying petal shape development in lotus (Nelumbo) by Jiaxin He, Jiaxin He, Yini Ma, Qingqing Liu, Rui Zhang, Guohong Huang, Dasheng Zhang, Fengluan Liu, Caixia Yang

Get full text

Multi-region brain transcriptomic analysis of amyotrophic lateral sclerosis reveals widespread RNA alterations and substantial cerebellum involvement by Natalie Grima, Andrew N. Smith, Claire E. Shepherd, Lyndal Henden, Thiri Zaw, Luke Carroll, Dominic B. Rowe, Matthew C. Kiernan, Ian P. Blair, Kelly L. Williams

“…Methods We generated 165 sample-matched post-mortem brain transcriptomes from 22 sporadic ALS patients with pTDP-43 pathological staging and 11 non-neurological controls. …”
Get full text

Combined transcriptome and metabolome analysis provides insight into the ERF073 – Malic acid network in pakchoi under submergence stress by Dan-dan Xi, Lu Gao, Li-ao Ge, Hong-fang Zhu, Li-ming Miao, Ding-yu Zhang, Chang-wei Zhang, Ying Li, Yan-xiao Dong, Xi-lin Hou, Yu-ying Zhu, Zhao-hui Zhang, Xiao-feng Li

“…Additionally, 553 commonly differentially expressed genes (DEGs) were found both in S1 vs H1 and S5 vs H5 at the stress stage, while 458 DEGs were commonly found in the two comparison groups at the recovery stage. …”
Get full text

Integrated hepatic transcriptomics and metabolomics identify Pck1 as a key factor in the broad dysregulation induced by vehicle pollutants by Gajalakshmi Ramanathan, Yuqi Zhao, Rajat Gupta, Siri Langmo, May Bhetraratana, Fen Yin, Will Driscoll, Jerry Ricks, Allen Louie, James A. Stewart, Timothy R. Gould, Timothy V. Larson, Joel Kaufman, Michael E. Rosenfeld, Xia Yang, Jesus A. Araujo

“…Expression microarrays and global metabolomics assessment were performed in the liver. An integrated transcriptomic and metabolomic analytical strategy was employed to dissect critical pathways and identify candidate genes that could dissect DE-induced pathogenesis. …”
Get full text

Transcriptome Analysis of <i>Sclerotium rolfsii</i>: Unraveling Impact of Glycolytic Pathway on Substrate Utilization and Microbial Polysaccharide Production by Jia Song, Junfeng Li, Chenrui Zhen, Juan Du, Rui Zhao, Bingqian Fan, Jiayi Hou, Bingning Gao, Yu Zheng, Linna Tu, Min Wang

“…In this study, we performed a transcriptomic analysis on the mycelium of <i>S. rolfsii</i> fermented with different carbon sources. …”
Get full text

Spatial transcriptomics reveals prognostically LYZ + fibroblasts and colocalization with FN1 + macrophages in diffuse large B-cell lymphoma by Liyuan Dai, Ning Lou, Liling Huang, Lin Li, Le Tang, Yuankai Shi, Xiaohong Han

“…Methods This study is a multi-omics approach, integrating spatial transcriptomics (n = 11), bulk transcriptomics (n = 2,499), immunohistochemistry (IHC, n = 37), multiplex immunofluorescence (mIF, n = 56), and plasma samples (n = 240) to identify and characterize fibroblast and tumor-associated macrophage subtypes in the TME. …”
Get full text

The hematopoietic function, histological characteristics, and transcriptome profiling of Wanxi white geese ovary during nesting and late-laying stages by Chunfang Zhao, Tao Jin, Kefeng Yang, Xinyu Liu, Man Ren, Deyong She, Qianqian Hu, Shenghe Li

Get full text

Accumulation differences of high-value ingredients in different phenotype Lonicera macranthoides: insights from integrative metabolome and transcriptome analyses by Juan Zeng, Juan Zeng, Yu Qing Long, Yu Qing Long, Jia Yuan Zhu, Jia Yuan Zhu, Xue Sen Fu, Xue Sen Fu, Jing Yu Zhang, Jing Yu Zhang, Jia Wei He, Jia Wei He, Xiao Rong Liu, Xiao Rong Liu, Zhi Hui Wang, Zhi Hui Wang, Qiao Zhen Tong, Qiao Zhen Tong, Xiang Dan Liu, Xiang Dan Liu, Xiang Dan Liu, Ri Bao Zhou, Ri Bao Zhou, Ri Bao Zhou

“…Nutrient and metabolites accumulation generally changed accompany with its floral development and opening. While the specific accumulation pattern and the underlying molecular regulatory networks remain unclear. …”
Get full text

Integrated single-cell and transcriptomic analysis of bone marrow-derived metastatic neuroblastoma reveals molecular mechanisms of metabolic reprogramming by Jing Chu, Rong Qin, Shu-Jing Wang, Qiang Wang, Qiang Wu

“…Single-cell RNA-sequencing data from 17 bone marrow aspirates of NB patients—with and without marrow infiltration—were retrieved from the GEO database, while bulk RNA-seq data from 155 NB tumor samples were obtained from the TARGET database. …”
Get full text

Integrative physiological and transcriptomic analysis provides insights on the molecular basis of ABA-enhanced drought tolerance in pear (Pyrus betulaefolia) by Guo-Ling Guo, An-Ran Luo, Yun-Hui Tan, Rui-Kang Yuan, Ting-Yue Luo, Pan-Pan Ma, Jun-Yu Zhan, Piao Han, Li Liu, Wei Heng, Zhenfeng Ye, Sheng Yang, Bing Jia

Get full text

Transcriptome analysis indicates improved adipose tissue function in growing Iberian pig fed olive by-products based diets by Patricia Palma-Granados, Patricia Palma-Granados, Juan M. García-Casco, Juan M. García-Casco, Ramón Peiró-Pastor, Cristina Óvilo, Miguel A. Delgado, Miguel A. Delgado, Fabián García, Adrián López-García, Adrián López-García, Elena González, María Muñoz

“…The aim of this study was to explore the transcriptome of backfat in Iberian pigs fed experimental diets based in olive by-products. …”
Get full text

Transcriptome analysis revealed that AcWRKY75 transcription factor reduced the resistance of kiwifruit to Pseudomonas syringae pv. actinidiae by Lixia Ye, Minmin Luo, Yafang Wang, Yafang Wang, Mengqi Yu, Mengqi Yu, Zhi Wang, Fuxi Bai, Xuan Luo, Li Li, Qiong Huang, Jue Peng, Qi Chen, Qinghong Chen, Lei Gao, Lei Zhang

“…Transient overexpression of AcWRKY75 in kiwifruit leaves reduced the resistance to Psa, while silencing AcWRKY75 by virus-induced gene silencing (VIGS) slightly enhanced the resistance to Psa. …”
Get full text

Integrative transcriptomic-physiological analysis deciphers nitrogen-mediated carbon reallocation balancing growth and flavonoid metabolism in Epimedium pubescens by Shangnian Liu, Shangnian Liu, Xiaojing An, Xiaojing An, Chaoqun Xu, Dongmei He, Xianen Li, Caixia Chen, Baolin Guo, De Xu, Juan Huang

“…This study provides molecular targets for precision nitrogen management to enhance both medicinal quality and yield, while establishing an integrative framework combining physiological and transcriptomic analyses to investigate metabolic trade-offs in non-model plants.…”
Get full text

A single-cell transcriptomic atlas of human lens epithelium: identification and functional insights into lens stem/progenitor cells by Yuzhou Gu, Lu Chen, Shuying Chen, Yuhao Wu, Shengjie Hao, Feiyin Sheng, Jiali Yuan, Zhenwei Qin, Di Wu, Yu Han, Zengying Yao, Zhijian Chen, I. Michael Wormstone, Yibo Yu, Junbin Qian, Qiuli Fu, Ke Yao

“…The 3 sub groups were labelled early, mid and late LECs and corresponded to stage 1, 3 and 4 in the path. While cell population demographics remained stable with age, transcriptomic changes in LECs were observed, including weaker intercellular crosstalk and adhesion, and fewer TACs in S phase. …”
Get full text

Integrative single-cell and spatial transcriptomics analysis reveals MDK-NCL pathway’s role in shaping the immunosuppressive environment of lung adenocarcinoma by Yu Fu, Song Li, Yikang Zhao, Xiran Zhang, Xiaolu Mao, Ran Xu

“…Spatial transcriptomics data facilitated the identification of distinct tumor niches, while immune infiltration and ligand-receptor interactions were analyzed using MCPcounter and Niches. …”
Get full text

Integrated Metabolome and Transcriptome Analysis Reveals the Key Bitter Substances of <i>Pleioblastus amarus</i> Shoots at Different Developmental Stages by Limei Gong, Weijin Shi, Chunyan Mou, Shixing Zhou, Lin Xiao, Hongling Hu, Lihua Tu, Guirong Hou, Wei Ding, Congde Huang, Gang Chen

“…Notably, BT2 exhibited upregulation of flavonoids, such as apigenin, while bitter amino acids, including phenylalanine and arginine, showed a marked increase in BT3. …”
Get full text

Transcriptome analyses reveal differences in the response to temperature in Florida and Northern largemouth bass (Micropterus spp.) during early life stages. by Moisés A Bernal, Gavin L Aguilar, Josh Sakmar, Sebastian N Politis, Savannah L Oglesby, Allen Nicholls, Anita M Kelly, Luke A Roy, Ian A E Butts

“…The main objective of this study was to determine the impact of thermal rearing conditions (21°C, 24°C, and 27°C) on gene expression of Florida and Northern LMB larvae at 8- and 28-days post hatch (DPH). Using de novo transcriptomes as a reference, our results suggest that gene expression differences for Florida LMB were mostly associated with temperature, while differences for Northern LMB were controlled by temperature and developmental stage. …”
Get full text

A Comprehensive Transcriptomic and Proteomics Analysis of Candidate Secretory Proteins in Rose Grain Aphid, <i>Metopolophium dirhodum</i> (Walker) by Atsbha Gebreslasie Gebrekidan, Yong Zhang, Julian Chen

“…The Rose grain aphid, a notable agricultural pest, releases saliva while feeding. Yet, there is a need for a comprehensive understanding of the specific identity and role of secretory proteins released during probing and feeding. …”
Get full text

UV-Induced Mutants of <i>Metarhizium anisopliae</i>: Improved Biological Parameters, Resistance to Stressful Factors, and Comparative Transcriptomic Analysis by Hao Gao, Yingjie Luo, Qiming Li, Jiaxuan Guo, Bin Wang

“…Among them, the mutant MaUV-22 exhibited enhanced tolerance to heat, oxidative, osmotic, and SDS stresses as well as increased virulence against <i>Galleria mellonella</i>. Moreover, the transcriptome analysis of MaUV-22 revealed that the expression of genes associated with the heat shock protein pathway, glutathione S-transferase, and thioredoxin reductase were increased dramatically, while the expression of genes related to the catalase and superoxide dismutase pathways was downregulated. …”
Get full text