CYCLONE: recycle contrastive learning for integrating single-cell gene expression data by Han Ji, Xinwei He, Hongwei Li

“…Abstract Background Combining single-cell transcriptome sequencing results from several batches reduces batch effect, which improves our understanding of cellular identity and function. …”
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Time-sensitive effects of quercetin on rat basophilic leukemia (RBL-2H3) cell responsiveness and intracellular signaling. by Mana Matsuo, Shuang Liu, Haruna Yamada, Erika Takemasa, Yasuyuki Suzuki, Masaki Mogi

“…We employed comprehensive transcriptome analysis and subsequent functional validation of key signaling pathways. …”
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Inhibition of the nucleolar RNA exosome facilitates adaptation to starvation. by Xi Feng, Xiaoman Wang, Shouhong Guang, Shanshan Pang, Haiqing Tang

“…RNA surveillance is crucial for the integrity of the transcriptome, whose defects are associated with several human diseases. …”
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Identification of individual components of a commercial wheat germ acid phosphatase preparation. by Veronica R Moorman, Alexandra M Brayton

“…Furthermore, it is shown that some of these correspond to previously isolated isozymes; one of which has been also previously shown by transcriptome data to be overexpressed in wheat seeds. …”
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Microtubule mechanotransduction refines cytomegalovirus interactions with and remodeling of host chromatin by Celeste D. Rosencrance, Derek Walsh

“…Here, chromatin conformation capture (Hi-C) revealed how cytomegalovirus alters chromosome organization at both large- and small-scales. Nascent transcriptomics further revealed how transcriptional changes correlate with genomic reorganization, while also uncovering infection-induced transcriptional dysregulation that contributes to the induction of neuronal gene signatures in infected fibroblasts. …”
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Human cytomegalovirus and neonatal infection by Shelley M. Lawrence

“…This Review will detail our understanding of human cytomegalovirus infection, with an in-depth discussion regarding the viral genome and transcriptome that contributes to its pathophysiology. …”
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AtMYB72 aggravates photosynthetic inhibition and oxidative damage in Arabidopsis thaliana leaves caused by salt stress by Hongrui Zhang, Yinuo Wu, Hongbo Zhang, Nan Sun, Hongjiao Zhang, Bei Tian, Tanhang Zhang, Kexin Wang, Xu Nan, Huiui Zhang

“…Phenotypic observation showed that the damage of overexpression strain was more serious than that of Col-0 after salt treatment, while the mutant strain showed less salt injury symptoms. …”
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GINS1 facilitates the development of lung adenocarcinoma via Wnt/β-catenin activation by Luyuan Ma, Rongyang Li, Pengyong Li, Wenhao Yu, Zhanpeng Tang, Libo Si, Hui Tian

“…Additionally, a series of experiments showed that silencing GINS1 led to less proliferation and migration of LUAD cell lines, while its overexpression enhanced tumor progression. …”
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SS31 alleviates LPS-induced acute lung injury by inhibiting inflammatory responses through the S100A8/NLRP3/GSDMD signaling pathway by Peiyao Luo, Quankuan Gu, Jianpeng Wang, Xianyong Li, Nana Li, Wei Yang, Xianglin Meng, Mingyan Zhao

“…Methods The study applied transcriptome sequencing, immunofluorescence, PCR, immunofluorescence and other methods to explore the mechanism of SS31 in LPS induced ALI. …”
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An enhanced gene function analysis platform for Gastrodia Elata integrating further omics data and analysis tools by Bingbing Pan, Jingjie Zhang, Jiangxin Yang, Hang Yang, Qi Pan, Panpan Zhu, Jun Li, Jiaotong Yang

“…GO and KEGG annotations were predicted using InterProScan and GhostKOALA, while gene families were identified with HMMER, iTAK, OrthoFinder, and KEGG annotations. …”
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Shared genetic architecture between stroke and blood lipids: a large-scale genome-wide cross-trait analysis by Wenya Bai, Guilin Zhou, Huan Jiang, Xuelian Li, Jianlin Shao

“…Two-sample MR analysis indicated that higher HDL-C levels were associated with reduced risks of stroke and IS, while elevated TG levels increased IS risk. In a transcriptome-wide association study, we identified one previously unreported pleiotropic gene (ALDH2). …”
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Multi-omics analysis reveals Lactobacillus and Indolelactic acid involved in small intestinal adaptation of piglet with short bowel syndrome by Weipeng Wang, Ying Lu, Bo Wu, Shicheng Peng, Wei Cai, Yongtao Xiao

“…The beneficial anaerobes from Bacillota and Bacteroidota were depleted while microorganisms from Verrucomicrobiota and Fusobacteriota were enriched in feces from SBS piglets. …”
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Expression of senescence-related CD161 promotes extranodal NK/T cell lymphoma by affecting T cell phenotype and cell cycle by Chengxun Jin, Xin Li, Chaohe Zhang

“…Compared with the control group, the expressions of CD4 and CD161 in the aging group were significantly increased, while the expression of CD8 was decreased. Transcriptome analysis revealed 2,843 differentially expressed genes (DEGs) between the control and aging groups, with 2,060 up-regulated and 783 down-regulated genes identified. …”
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Multi-omics investigation of Porphyromonas gingivalis exacerbating acute kidney injury through the gut-kidney axis by Ling Dong, Zhaoxin Ji, Jing Sun, Jiangqi Hu, Qingsong Jiang, Wei Wei

“…In our study, AKI was induced in mice through ischemia-reperfusion injury while administering oral infection with P. gingivalis. …”
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IGF2BP3 prefers to regulate alternative splicing of genes associated with the progression of gastric cancer in AGS cells by Xiangyue Zeng, Yu Zhang, Tiannake Shapaer, Abulajiang Abudoukelimu, Zeliang Zhao, Binlin Ma

“…IGF2BP3, as a multifunctional RNA binding protein, is involved in regulating alternative splicing (AS) and m6A modification, and plays a carcinogenic role in the development of gastric cancer, while little is known about the impact of IGF2BP3 on alternative splicing in gastric cancer cells and the underlying mechanism. …”
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The role of KLF4 in human primordial germ cell development by Sun-Min Lee, Merrick Pierson Smela, M. Azim Surani

“…We demonstrate that the depletion of KLF4 reduces the efficiency of hPGCLC specification, resulting in hPGCLCs with an aberrant transcriptome. Cut-and-run and transcriptomic analyses reveal that KLF4 represses somatic markers involved in neuronal and endodermal differentiation while promoting the expression of genes associated with PGC specification, such as PAX5, and epigenetic regulators, including DNMT3L and REST. …”
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Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements by Benjamin J. Patty, Rinku Dhungana, Sarah J. Hainer

“…We find that paired mRNAs and eRNAs are co-regulated, while mRNAs and uaRNAs sharing a promoter are independently regulated by remodelers. …”
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Identification of novel proteins associated with intelligence by integrating genome-wide association data and human brain proteomics. by Zheng Zhang, Yousong Zhu, Junlong Zhang, Wenbin He, Cheng Han

“…While genome-wide association studies (GWAS) have identified genetic variants associated with intelligence, their biological mechanisms remain largely unexplored. …”
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Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana. by Dazhe Meng, Manu Dubin, Pei Zhang, Edward J Osborne, Oliver Stegle, Richard M Clark, Magnus Nordborg

“…We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. …”
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Tissue specific role of ABCA1 in lung cholesterol homeostasis under high-cholesterol diet by Jian Ma, Jian Ma, Zhongwen Gong, Hong Lu, Han Yang, Shengquan Wang, Qian Zhu, Hongya Liu, Yongjia Li, Yuemei Zhang, Xuemei Lian, Xuemei Lian

“…However, their tissue-specific roles, particularly in the lung, under high-cholesterol diet (HCD) conditions remain unclear.ObjectiveUsing the liver as a reference, this study aimed to investigate the tissue-specific regulation of ABCA1 in the lung under HCD or CYP27A1 knockout (KO) conditions, and to explore its potential regulatory mechanism.MethodsCYP27A1 KO and wild-type (WT) mice on a C57BL/6J background were fed either a normal diet (ND) or HCD for 12 weeks. Transcriptome sequencing (RNA-seq) was conducted on lung tissue samples.ResultsHCD feeding in WT mice caused significant hepatic lipid accumulation, while no notable lipid deposition was observed in lung tissue. …”
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