Identifying Key Biomarkers and Immune Infiltration in Female Patients with Ischemic Stroke Based on Weighted Gene Co-Expression Network Analysis by Haipeng Xu, Kelin He, Rong Hu, YanZhi Ge, Xinyun Li, Fengjia Ni, Bei Que, Yi Chen, Ruijie Ma

“…Moreover, the “Cell type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT)” was used to examine the distribution pattern of immune subtypes in female patients with IS and normal controls, revealing a new potential target for clinical treatment of the disease.…”
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Progress in plant genome sequencing: research directions by M. K. Bragina, D. A. Afonnikov, E. A. Salina

“…In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. …”
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STK3 Suppresses Ovarian Cancer Progression by Activating NF-κB Signaling to Recruit CD8+ T-Cells by Xiangyu Wang, Fengmian Wang, Zhi-Gang Zhang, Xiao-Mei Yang, Rong Zhang

“…Bisulfite sequencing PCR analysis was performed to validate the methylation of STK3 in ovarian cancer. RNA sequencing and gene set enrichment analysis (GSEA) were used to compare the transcriptome changes in the STK3 overexpression ovarian cancer and control cells. …”
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Differential pathological changes in colon microenvironments in acute and chronic mouse models of inflammatory bowel disease by NaYeon Ham, Minji Park, Young-An Bae, Eui-Ju Yeo, YunJae Jung

“…In contrast, the chronic phase was characterized by tissue remodeling, with a significant increase in M2 macrophages and lymphocytes. RNA-sequencing revealed genetic changes in acute and chronic colitis, marked by the maintenance of genomic integrity in the acute phase and extracellular matrix dynamics in the chronic phase. …”
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Genetic tracking of Crimean-Congo haemorrhagic orthonairovirus in Hyalomma population infesting cattle in Nigeria. by Oluwafemi Babatunde Daodu, Joseph Ojonugwa Shaibu, Rosemary Ajuma Audu, Daniel Oladimeji Oluwayelu

“…Blood samples and Hyalomma ticks were collected from cattle, with ticks identified to species, pooled, and homogenized for RNA extraction. The CCHFV S-segment was detected using specific primers via reverse transcriptase polymerase chain reaction, followed by sequencing of amplicons. …”
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Staphylococcus Derived from Desert and Its Solidified Ability on Aeolian Sandy Soil by Yu Gao, De Yao, Cuiyan Wang, Yanxing Wang, Chi Li

“…The autogenous mineralized strain was isolated and purified from desert Aeolian sandy soil, and the strain was identified as Staphylococcus using 16SrRNA sequence homology. It is a kind of mineralized bacteria seldom used in geotechnical engineering at present, and it was found to have good mineralization ability; the living conditions of Staphylococcus were optimized. …”
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Enhanced ferroptosis sensitivity promotes the formation of highly myopic cataract via the DDR2-Hippo pathway by Dongling Guo, Yu Du, Xin Liu, Dan Li, Ling Wei, Xiangjia Zhu

“…In HMC lens epithelia, levels of Fe2+ and lipid peroxidation were found elevated, with increased vulnerability towards ferroptosis as revealed by transmission electron microscopy. Mechanistically, RNA sequencing of HMC lens epithelial samples identified up-regulated expression of discoidin domain receptor tyrosine kinase 2 (DDR2) as a key factor, which could enhance ferroptosis sensitivity via the Src-Hippo pathway. …”
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Transcriptome Analysis of Cryptolestes ferrugineus under Low-temperature Stress by WU Tian-yi, WU Yi, FANG Zhi-yi, ZHANG Xiao-pei, WANG Fu-ling, XUE Ding-rong

“…Combining PacBio Iso Sequencing and Illumina RNA Sequencing, 10,508 full-length transcripts were obtained, with 9,523 successfully annotated. …”
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DNA Ligase IV Prevents Replication Fork Stalling and Promotes Cellular Proliferation in Triple Negative Breast Cancer by Rashmi R. Joshi, Sk Imran Ali, Amanda K. Ashley

“…We depleted Lig4 using siRNA and confirmed our knockdown by qPCR and western blotting. …”
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Characterization of covalent inhibitors that disrupt the interaction between the tandem SH2 domains of SYK and FCER1G phospho-ITAM. by Frances M Bashore, Vittorio L Katis, Yuhong Du, Arunima Sikdar, Dongxue Wang, William J Bradshaw, Karolina A Rygiel, Tina M Leisner, Rod Chalk, Swati Mishra, C Andrew Williams, Opher Gileadi, Paul E Brennan, Jesse C Wiley, Jake Gockley, Gregory A Cary, Gregory W Carter, Jessica E Young, Kenneth H Pearce, Haian Fu, Emory-Sage-SGC TREAT-AD Center, Alison D Axtman

“…RNA sequencing and genetic data support spleen tyrosine kinase (SYK) and high affinity immunoglobulin epsilon receptor subunit gamma (FCER1G) as putative targets to be modulated for Alzheimer's disease (AD) therapy. …”
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Endothelial STAT3 Modulates Protective Mechanisms in a Mouse Ischemia-Reperfusion Model of Acute Kidney Injury by Shataakshi Dube, Tejasvi Matam, Jessica Yen, Henry E. Mang, Pierre C. Dagher, Takashi Hato, Timothy A. Sutton

“…Moreover, important proximal tubular adaptive mechanisms to injury were diminished in association with decreased tissue mRNA levels of the epithelial cell survival cytokine IL-22. …”
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Bioinformatic Prediction of Novel microRNAs Encoded in Krüppel-like Factor 4 Gene by Mina Zahiri, Maryam Hassanlou, Amir-Reza Javanmard, Nooshin Bijari

“…Advanced bioinformatics methods, including SSCprofiler website, were used to predict stem-loop structures in KLF4 gene, and MatureBayes website was used to predict the mature sequence of microRNAs, which indicate potential miRNA candidates. Using the RNAfold website, the stem-loop structure of microRNAs was determined. …”
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Identification of the Genomics and Transcriptomics Regulators of the DNA Damage Response in Breast Cancer by Mehdi Sadeghi, Mohammad Reza Karimi, Amir Hossein Karimi

“…By identifying differentially expressed genes in single-cell cancer cell populations inherently different in DNA damage response, further clustering bulk RNA-sequencing samples based on the expression of these genes, and performing network and enrichment analysis at the bulk level, we have characterized breast cancer samples based on their DNA damage response. …”
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ADF1 and BEAF-32 chromatin proteins affect nucleosome positioning and DNA decompaction in 61C7/C8 interband region of Drosophila melanogaster polytene chromosomes by M. B. Schwartz (Berkaeva), T. E. Pankova, S. A. Demakov

“…We also find that ADF1 and BEAF-32 binding sites are essential for the rescue of lethality caused by the null allele of bantam microRNA gene located in the region 61C7/C8.…”
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Long Noncoding RNAs, Chromatin, and Development by Daniel P. Caley, Ryan C. Pink, Daniel Trujillano, David R. F. Carter

“…Better characterization of the lncRNA-protein "interactome" may eventually lead to a new molecular toolkit, allowing researchers and clinicians to modulate the genome at the epigenetic level to treat conditions such as cancer.…”
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Analysis of the Salivary Microbiome in Obstructive Sleep Apnea Syndrome Patients by Peizeng Jia, Jianyin Zou, Shankai Yin, Feng Chen, Hongliang Yi, Qian Zhang

“…Saliva was collected from 15 OSAS patients and nine healthy controls, and bacterial genomic DNA was extracted for 16S rRNA amplicon sequencing based on the Illumina platform. …”
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Polymorphism rs3828903 within MICB Is Associated with Susceptibility to Systemic Lupus Erythematosus in a Northern Han Chinese Population by Yue-miao Zhang, Xu-jie Zhou, Fa-juan Cheng, Yuan-yuan Qi, Ping Hou, Ming-hui Zhao, Hong Zhang

“…In silico analyses predicted a higher affinity to transcription factors for allele G (risk) and cis-expression quantitative trait loci (cis-eQTL) effects of rs3828903 in multiple tissues (P ranging from 2.79×10-6 to 6.27×10-38). Furthermore, higher mRNA expressions of MICB were observed in B cells, monocytes, and renal biopsies from SLE patients compared to controls. …”
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Dietary Quercetin Regulates Gut Microbiome Diversity and Abundance in <i>Apis cerana</i> (Hymenoptera Apidae) by Haodong Wu, Conghui Ji, Ruisheng Wang, Lijiao Gao, Wenhua Luo, Jialin Liu

“…Gut samples were collected on the 5th and 9th days, subjected to a polymerase chain reaction and 16S rRNA sequencing, and analyzed. After 5 days of quercetin treatment, the diversity of the honeybee gut microbiota was altered, and total bacterial copies and <i>Lactobacillus</i> abundance significantly decreased at high quercetin concentrations (151.2 and 75.6 mg/L). …”
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Identification of Signal Pathways and Hub Genes of Pulmonary Arterial Hypertension by Bioinformatic Analysis by Rui-Qi Wei, Wen-Mei Zhang, Zhe Liang, Chunmei Piao, Guangfa Zhu

“…Significant KEGG pathway enrichment included ribosome biogenesis in eukaryotes, RNA transport, proteoglycans in cancer, dilated cardiomyopathy, rheumatoid arthritis, vascular smooth muscle contraction, focal adhesion, regulation of the actin cytoskeleton, and hypertrophic cardiomyopathy. …”
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RNASeq analysis of drought-stressed guayule reveals the role of gene transcription for modulating rubber, resin, and carbohydrate synthesis by Chen Dong, Grisel Ponciano, Naxin Huo, Yong Gu, Daniel Ilut, Colleen McMahan

“…To better understand how drought influences rubber biosynthesis at the molecular level, a comprehensive transcriptome database was built from drought-stressed guayule stem tissues using de novo RNA-seq and genome-guided assembly, followed by annotation and expression analysis. …”
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