Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity by Antony Cougnoux, Loay Mahmoud, Per A. Johnsson, Alper Eroglu, Louise Gsell, Jakob Rosenbauer, Rickard Sandberg, Jean Hausser

“…To address this, we combine dye diffusion, the Smart-seq3xpress protocol for deep single-cell gene expression profiling, and dedicated probabilistic inference methods into diffusion Smart-seq3 (Smart-seq3D), to reveal the transcriptome of single cells along with their position along the core-periphery axis of spheroids. …”
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Hyperhomocysteinemia-induced VCID results in visual deficits, reduced neuroinflammation and vascular alterations in the retina by Erica M. Weekman, Colin B. Rogers, Tiffany L. Sudduth, Donna M. Wilcock

“…Finally, neuroinflammatory and cardiovascular gene expression was measured using NanoString’s nCounter system. …”
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Ascorbic acid alleviates reproductive toxicity of di-(2-ethyl hexyl) phthalate in female Wistar rats by Kalaivani Manokaran, Ravi Sankar Bhaskaran, Jayesh Mudgal, Prabu Paramasivam, Sachin Shetty, Deepak Nayak, Sunitha Carnelio, Vennila Jaganathan, Dharani Abirama Sundari Shanmugam, Karkala Sreedhara Ranganath Pai

“…Blood and ovarian tissues were collected to assess serum reproductive hormones, gonadotropin receptor gene expression, oxidative stress markers, and apoptosis. …”
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LASSO–MOGAT: a multi-omics graph attention framework for cancer classification by Fadi Alharbi, Aleksandar Vakanski, Murtada K. Elbashir, Mohanad Mohammed

“…Combining gene expression data with other types of omics data has been reported by numerous works to improve cancer classification outcomes. …”
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A Systematic Pan-Cancer Analysis of YY1 Aberrations and their Relationship with Clinical Outcome, Tumor Microenvironment, and Therapeutic Targets by Xinghao Fu, Feihong Ji, Qi He, Xinguang Qiu

“…We first explored the potential carcinogenic effect of YY1 in 33 cancers using the cancer genome atlas (TCGA) project and gene expression omnibus (GEO) datasets in this research. …”
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A Robust Hybrid Approach Based on Estimation of Distribution Algorithm and Support Vector Machine for Hunting Candidate Disease Genes by Li Li, Hongmei Chen, Chang Liu, Fang Wang, Fangfang Zhang, Lihua Bai, Yihan Chen, Luying Peng

“…The results showed that the proposed method provides new computational strategy for hunting candidate disease genes from the profile data of disease gene expression. The selected candidate disease genes may help to improve the diagnosis and treatment for diseases.…”
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Bioinformatics Method Was Used to Analyze the Highly Expressed Gene FAM83A of Breast Cancer in Young Women by Yongzhe Tang, Hao Wang, Qi He, Yuanyuan Chen, Jie Wang

“…The active site of PLDc and the functional domain of DUF1669 can be involved in signal transduction and gene expression regulation in tumorigenesis and metastasis. …”
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Postrecruitment Function of Yeast Med6 Protein during the Transcriptional Activation by Mediator Complex by Gwang Sik Kim, Young Chul Lee

“…In an artificial recruitment assay, Mediator containing a LexA-fused wild-type Med6p or Med6p-Δ5 was recruited to the lexA operator region with TBP and activated reporter gene expression. However, the recruitment of Mediator containing LexA-Med6p-Δ6 to lexA operator region resulted in neither TBP recruitment nor reporter gene expression. …”
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Increased N-Ethylmaleimide-Sensitive Factor Expression in Amygdala and Perirhinal Cortex during Habituation of Taste Neophobia by Beatriz Gómez-Chacón, Fernando Gámiz, Thomas C. Foster, Milagros Gallo

“…Total RNA was extracted and gene expression was measured by quantitative PCR (qPCR) using TaqMan gene expression assays. …”
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The Dynamic DNA Demethylation during Postnatal Neuronal Development and Neural Stem Cell Differentiation by Huikang Tao, Pei Xie, Yuhang Cao, Liqi Shu, Liping Li, Junchen Chen, Guangfeng Tian, Yingliang Zhuang, Qiang Shu, Xuekun Li

“…DNA demethylation displayed dynamic features during postnatal neuronal development and the differentiation of aNSCs of mice, which could contribute to appropriate gene expression.…”
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Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications by Farhana Manzoor, Cyruss A. Tsurgeon, Vibhuti Gupta

“…RNA sequencing (RNA-seq) has emerged as a prominent resource for transcriptomic analysis due to its ability to measure gene expression in a highly sensitive and accurate manner. …”
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Symbiotic Root-Endophytic Soil Microbes Improve Crop Productivity and Provide Environmental Benefits by Gary E. Harman, Norman Uphoff

“…Although these exhibit quite different “lifestyles” when inhabiting plants, all induce beneficial systemic changes in plants’ gene expression that are surprisingly similar. For example, all induce gene expression that produces proteins which detoxify reactive oxygen species (ROS). …”
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RETRACTED ARTICLE: Screening and identification of susceptibility genes for cervical cancer via bioinformatics analysis and the construction of an mitophagy-related genes diagnosti... by Zhang Zhang, Fangfang Chen, Xiaoxiao Deng

“…Method We initially collected a large amount of genomic data, including gene expression profile and single nucleotide polymorphism (SNP) data, from the control group and Cervical cancer (CC) patients. …”
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Arginine–NO pathway modulated energy metabolism in the hepatopancreas and muscle of female Litopenaeus vannamei by Haitao Fan, Xin Zhang, Yanan Yin, Lefei Jiao

“…Above results were further confirmed by gene expression. In addition, shrimp were injected with dsGFP and dsNOS for 48 h and successfully constructed the RNA interference model. …”
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Antitumor Activities of Aqueous Cinnamon Extract on 5637 Cell Line of Bladder Cancer through Glycolytic Pathway by Zeynab Aminzadeh, Nasrin Ziamajidi, Roghayeh Abbasalipourkabir, Sajedeh Daei, Sobhan Helbi, Abbas Moridnia

“…Aqueous extract of Cinnamon significantly decreased ErbB2, HSF1, and LDHA gene expression and also decreased the protein level of HSF1 and LDHA, LDH activity, glucose consumption, and lactate production dose-dependently (p<0.05). …”
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Transcriptome sequencing reveals regulatory genes associated with neurogenic hearing loss by Fengfeng Jia, Fang Wang, Song Li, Yunhua Cui, Yongmei Yu

“…However, comprehensive studies investigating the differential gene expression and regulatory mechanisms associated with hearing loss are lacking, particularly in the context of diverse patient samples. …”
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A Review on The Impact of Thermal Stress on Fish Biochemistry by Manoj Kumar Pati, Mohammad Aftabuddin, Prasun Roychowdhury

“…Fish employ strategies to cope with thermal stress, including altering gene expression, metabolite profiles, cellular signaling, and enzyme activity. …”
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Expression of Shelterin Component POT1 Is Associated with Decreased Telomere Length and Immunity Condition in Humans with Severe Aplastic Anemia by Ting Wang, Shu-chong Mei, Rong Fu, Hua-quan Wang, Zong-hong Shao

“…No differences in the gene expression of the other Shelterin components—TRF1, TRF2, TIN2, TPP1, and RAP1—were identified. …”
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A Comparative Study on Growth Performance, Body Composition, and Liver Tissue Metabolism Rearing on Soybean Lecithin-Enriched Artemia Nauplii and Microdiet in Rock Bream (Oplegnath... by Pian Zhang, Peng Tan, Lei Zhang, Wenliang Zhu, Ruiyi Chen, Ligai Wang, Dongdong Xu

“…RNA sequencing revealed that feeding with the MD primarily increased the expression of lipogenesis-related genes and protein translation-related gene expression in the liver tissue. Notably, feeding with MD significantly increased ribosome biogenesis-related genes as well as mitochondria synthesis-related gene expression, indicating a high protein anabolism rate and high energy production in liver tissue. …”
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Migration, Proliferation, and Differentiation of Cord Blood Mesenchymal Stromal Cells Treated with Histone Deacetylase Inhibitor Valproic Acid by Leah A. Marquez-Curtis, Yuanyuan Qiu, April Xu, Anna Janowska-Wieczorek

“…We found that in MSC, VPA increased (i) the gene and total protein expression of CXCR4 and CXCR7 and primed migration towards a low gradient of SDF-1, (ii) the gene expression of MMP-2 and secretion and activation of proMMP-2, (iii) the proliferation and gene expression of pluripotency markers SOX2 and Oct-4, and exposure to lower concentrations of VPA (≤5 mM) had no effect on their differentiation to osteocytes and chondrocytes. …”
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