Differential gene expression analysis in patients with primary hyperhidrosis by Ting Pu, Muhammad Ameen Jamal, Muhammad Nauman Tahir, Salman Ullah, Maher Un Nisa Awan, Asif Shahzad, Faisal Mahmood

“…Microarray data analysis on anhidrosis was done using GEO2R database as well as the anhidrosis datasets available on Gene Exression Omnibus (GEO). …”
Get full text

Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference by Yinlei Lei, Min Li, Han Zhang, Yu Deng, Xinyu Dong, Pengyu Chen, Ye Li, Suhua Zhang, Chengtao Li, Shouyu Wang, Ruiyang Tao

“…In this study, 220 samples, consisting of sterile swabs from palmar skin and oral and nasal cavities were collected from Chinese Han individuals living in Shanghai, Chifeng, Kunming, and Urumqi, representing the geographic regions of east, northeast, southwest, and northwest China. The full-length 16S rRNA gene of the microbiota in each sample was sequenced using the PacBio single-molecule real-time sequencing platform, followed by clustering the sequences into operational taxonomic units (OTUs). …”
Get full text

Integrated Single-Cell and Spatial Transcriptomic Analysis Identifies ISR-Related Genes Driving Immune Regulation in Parkinson’s Disease by Jiang H, Zhang X, Feng S, Feng W

“…The Integrated Stress Response (ISR) helps cells cope with stress and is linked to neurodegenerative diseases, but its role in PD is not well known. In this study, we used advanced transcriptomic techniques, including single-cell RNA sequencing and spatial transcriptomics, to analyze gene expression patterns in PD. …”
Get full text

Combined genome and transcriptome analysis identifies molecular signatures of aortic disease in patients with Marfan syndrome by Katherine B. Stanley, Alexa V. Mederos, Ethan H. Barksdale, Joel S. Corvera, Joshua L. Davis, Fang Fang, Hongyu Gao, Courtney E. Vujakovich, Yunlong Liu, Stephanie M. Ware, Benjamin J. Landis

“…Smooth muscle cells (SMCs) were cultured directly from the proximal aortic tissues of MFS cases undergoing aortic root replacement and controls during heart transplant. Genome sequencing (GS) analysis was combined with mRNA-sequencing (mRNA-seq) and single-cell gene expression profiling of SMCs. …”
Get full text

The novel diagnostic markers for systemic lupus erythematosus and periodontal disease by Xuedi Cheng, Jinfeng Zhang, Jiali Hou, Xiaocui Han, Bin Han, Jun Zhou, Zhongjun Wang, Junzheng Wang

“…Finally, hub genes were validated using additional datasets, single-cell RNA sequencing (scRNA-seq) data, and immunohistochemistry (IHC) experiments.ResultsUsing WGCNA, we identified significant correlation modules and overlapping module genes, which were subjected to differential expression analysis in different datasets. …”
Get full text

Combining single-cell analysis and molecular docking techniques to construct a prognostic model for colon adenocarcinoma and uncovering inhibin subunit βb as a novel therapeutic ta... by Qinqing Wu, Qinqing Wu, Lu Ye, Yuwei Wu, Mengyu Zhao, Mengyu Zhao, Jiaxin Lu, Yanping Yu, Yanping Yu, Yixiao Niu, Yixiao Niu, Luxiao Zhang, Peijun Zuo, Peijun Zuo

“…We also investigated the roles and interactions of these genes in the tumor microenvironment by analyzing single-cell RNA sequencing data. Additionally, we employed molecular docking techniques to evaluate the potential of inhibin subunit beta B (INHBB) as therapeutic targets and to assess the binding affinity of candidate drugs. …”
Get full text

Integrated single-cell analysis reveals distinct epigenetic-regulated cancer cell states and a heterogeneity-guided core signature in tamoxifen-resistant breast cancer by Kun Fang, Aigbe G. Ohihoin, Tianxiang Liu, Lavanya Choppavarapu, Bakhtiyor Nosirov, Qianben Wang, Xue-Zhong Yu, Sailaja Kamaraju, Gustavo Leone, Victor X. Jin

“…Abstract Background Inter- and intra-tumor heterogeneity is considered a significant factor contributing to the development of endocrine resistance in breast cancer. Recent advances in single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) allow us to explore inter- and intra-tumor heterogeneity at single-cell resolution. …”
Get full text

Expressed mutated genes in Sezary syndrome and their potential prognostic value in patients treated with extracorporeal photopheresis by Cristina Cristofoletti, Giulia Salvatore, Cristian Bassi, Massimo Negrini, Giovanni Luca Scaglione, Luca Mazzarella, Gianmaria Frigè, Ylenia Aura Minafò, Martina Fioretti, Alessandro Monopoli, Maria Pina Accetturi, Maria Antonietta Pilla, Cosimo Di Raimondo, Alessandra Frezzolini, Enrico Scala, Stefania D’Atri, Giandomenico Russo, Maria Grazia Narducci

“…It is characterized by a complex and heterogeneous profile of genetic alteration ns that has so far precluded the development of a specific and definitive therapeutic intervention.MethodsDeep-RNA-sequencing (RNA-seq) data were used to analyze the single nucleotide variants (SNVs) carried by 128 putative CTCL-driver genes, previously identified as mutated in genomic studies, in longitudinal SS samples collected from 17 patients subjected to extracorporeal photopheresis (ECP) with Interferon-α. …”
Get full text

Three new sequences of Ostrea stentina and the evolution of the mitogenome of the Ostreinae clams (Ostreidae, Bivalvia) by Daniele Corrain, Daniele Corrain, Rafaella Franch, Rafaella Franch, Massimiliano Babbucci, Massimiliano Babbucci, Davide Tagliapietra, Irene Guarneri, Marco Sigovini, Valentina Bonfatti, Tomaso Patarnello, Tomaso Patarnello, Enrico Negrisolo, Enrico Negrisolo, Enrico Negrisolo

“…The study of these mitogenomic arrangements identified gene blocks that were present in the mitogenome of the last common ancestor of the Ostreidae. The comparative analysis allowed identifying peculiar features of the mitogenomes of Ostreinae as well as of their protein coding genes, tRNAs genes, rRNA genes, and control regions. …”
Get full text

Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences. by Oriya Vardi, Inbal Shamir, Elisheva Javasky, Alon Goren, Itamar Simon

“…Although this bias is obvious only when performing paired end sequencing, it affects single end sequenced samples as well. …”
Get full text

Decoding Cellular Landscapes: Unravelling Periodontitis and Periapical Periodontitis at the Single-Cell Frontier by Yuan Li, Jun Wang, Yu Zhang, Dengke Li, Wuyang Zhang, Xuebing Li, Bolun Zhang, Kaijin Hu, Jianfei Yan, Yang Xue

“…Objective: Elucidate differences in key gene expression and cellular heterogeneity in alveolar bone between periodontitis (PD) and periapical periodontitis (PP) by analysing single-cell RNA sequencing data. Methods: Single-cell RNA sequencing datasets for PD (GSE171213) and PP (GSE181688) were obtained from the Gene Expression Omnibus and analysed. …”
Get full text

Genome-wide quantitative dissection of an arthropod segmented body plan at single-cell resolution by Takanori Akaiwa, Hiroki Oda, Yasuko Akiyama-Oda

“…Here, we present high-quality quantitative data from single-nucleus RNA sequencing of spider Parasteatoda tepidariorum embryos at late stage 5 and stage 7, a critical period of emergence of segmental units along the anterior–posterior (AP) axis. …”
Get full text

Single-cell profiling of SLC family transporters: uncovering the role of SLC7A1 in osteosarcoma by Yan Liao, Junkai Chen, Hao Yao, Ting Zheng, Jian Tu, Weidong Chen, ZeHao Guo, Yutong Zou, Lili Wen, Xianbiao Xie

“…Solute carrier (SLC) family transporters have been implicated in the malignant progression of a variety of tumors, however, their specific role in osteosarcoma remains poorly understood. Methods The single-cell sequencing data from GSE152048 and GSE162454, along with RNA-seq from the TARGET and GSE21257 cohorts, were utilized for the analysis in this study. …”
Get full text

Targeting glycolysis in esophageal squamous cell carcinoma: single-cell and multi-omics insights for risk stratification and personalized therapy by Yan Wang, Yan Wang, Yunjie Shi, Yunjie Shi, Xiao Hu, Xiao Hu, Chenfang Wang, Chenfang Wang

“…BackgroundEsophageal squamous cell carcinoma (ESCC) is closely linked to aberrant glycolytic metabolism, a hallmark of cancer progression, immune evasion, and therapy resistance. This study employs single-cell transcriptomics and multi-omics approaches to unravel glycolysis-mediated mechanisms in ESCC, with a focus on risk stratification and therapeutic opportunities.MethodsData from TCGA and GEO databases were integrated with single-cell RNA sequencing, bulk RNA sequencing, as well as clinical datasets to investigate glycolysis-associated cell subtypes and their clinical implications in ESCC. …”
Get full text

48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis by Yuwei Qin, Zhijian Liu, Shiqi Gao, Carlos Martínez-Vasallo, Yanping Long, Xinlong Zhu, Bin Liu, Ya Gao, Xiaodong Xu, Maria A. Nohales, Qiguang Xie, Jixian Zhai

“…To bridge this gap, we employ time-lapse single-nucleus RNA sequencing (snRNA-seq) on Arabidopsis seedlings collected over a 48-hour window at 4-hour intervals, as well as over a 24-hour day at 2-hour intervals, yielding a total of over 77,142 and 130,000 nuclei. …”
Get full text

Spatial transcriptomic and morpho-functional information derived from single mouse FFPE slides allows in-depth fingerprinting of lung fibrosis by Erica Ferrini, Costanza Bonfini, Giovanna Marchese, Martina Buccardi, Matteo Zoboli, Primetta Faccioli, Nicola Sverzellati, Gino Villetti, Simone Ottonello, Maria Ravo, Franco F. Stellari

“…Abstract Background Transcriptome profiling by RNA sequencing (RNAseq) can provide insightful information on the molecular processes underlying disease development and progression. …”
Get full text

EXPLORING THE ROLE OF GUT MICROBIOTA IN PATIENTS WITH MULTIPLE SCLEROSIS IN UKRAINE: A CROSS-SECTIONAL STUDY by Kateryna P. Potapova, Larysa I. Sokolova

“…Microbiome analysis was performed via 16S rRNA gene sequencing on the Illumina MiSeq platform. …”
Get full text

Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes by Hannah Demond, Soumen Khan, Juan Castillo-Fernandez, Courtney W. Hanna, Gavin Kelsey

“…We develop a classifier that can be used to infer chromatin status in single-cell or bulk RNA-seq data, enabling identification of altered chromatin transition in genetic knock-outs, and a quality control to identify skewed NSN-SN proportions that could otherwise confound differential gene expression analysis. …”
Get full text

Significance of KLK7 expression, polymorphisms, and function in sheep horn growth by Mingzhu Shan, Hao Li, Xinyue Li, Guoqing Zhang, Jianxin Shi, Pingjie Feng, Lisheng Zhou, Zhangyuan Pan, Mingxing Chu

“…Results This study utilized RNA sequencing (RNA-Seq) data to analyze the expression levels of the KLK7 gene across different species, as well as among different breeds, tissue types, and genders in sheep. …”
Get full text

Genetic diversity of single-celled microorganism Blastocystis sp. and its associated gut microbiome in free-ranging marine mammals from North-Western Mediterranean Sea by Marianna Marangi, Sonia Boughattas

Get full text