Comprehensive analysis of anoikis-related genes in diagnosis osteoarthritis: based on machine learning and single-cell RNA sequencing data by Jun-Song Zhang, Run-Sang Pan, Guo-Lu Li, Jian-Xiang Teng, Hong-Bo Zhao, Chang-Hua Zhou, Ji-Sheng Zhu, Hao Zheng, Xiao-Bin Tian

“…The XGB, SVM, RF, and GLM models identified five hub genes (CDH2, SHCBP1, SCG2, C10orf10, P FKFB3), and the diagnostic model built using these five genes performed well in the training and validation cohorts. analysing single-cell RNA sequencing data from GSE152805, including 25,852 cells of 6 OA cartilage.…”
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Single-Cell RNA-Sequencing Analysis Provides Insights into IgA Nephropathy by Ming Xia, Yifu Li, Yu Liu, Zheng Dong, Hong Liu

“…In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) technology has provided the high-resolution and rich data necessary to elucidate disease characteristics and enabled the analysis of complex interactions between individual cells and cell types. …”
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Exploring the impact of cuproptosis on prostate cancer prognosis via RNA methylation regulation based on single cell and bulk RNA sequencing data by Junchao Wu, Junchao Wu, Junchao Wu, Wentian Wu, Jiaxuan Qin, Jiaxuan Qin, Jiaxuan Qin, Ziqi Chen, Ziqi Chen, Ziqi Chen, Rongfang Zhong, Peng Guo, Song Fan, Song Fan, Song Fan

“…In conjunction with this, we conducted single-cell RNA sequencing (scRNA-seq) analyses to investigate underlying mechanisms and evaluate the degree of immune infiltration, as well as to assess patients’ responses to diverse chemotherapy agents. …”
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Analysis of histone modifications in key cellular subpopulations in the context of azoospermia using spermatogenic single-cell RNA-seq data by Qiu Wang, Qiu Wang, Hong Yang, Fang Li, Fang Li, Song Ge, Song Ge, Ling Ji, Ling Ji, Xiaofeng Li, Xiaofeng Li

“…IntroductionThe molecular underpinnings of non-obstructive azoospermia (NOA), a severe form of male infertility characterized by the absence of sperm in the ejaculate, remain unclear.MethodsIn this study, we demonstrate the role of histone modifications within specific testicular cell subpopulations in NOA using single-cell RNA sequencing (scRNA-seq) data.ResultsBased on scRNA-seq analysis of the data acquired from the Gene Expression Omnibus (GSE149512), we identified nine distinct cell types and revealed significant compositional differences between the NOA and control testicular tissues. …”
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Comprehensive Analysis of Programmed Cell Death-Related Genes in Diagnosis and Synovitis During Osteoarthritis Development: Based on Bulk and Single-Cell RNA Sequencing Data by Zhou J, Jiao S, Huang J, Dai T, Xu Y, Xia D, Feng Z, Chen J, Li Z, Hu L, Meng Q

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Consistently processed RNA sequencing data from 50 sources enriched for pediatric data by Holly C. Beale, Katrina Learned, Ellen T. Kephart, A. Geoffrey Lyle, Anouk van den Bout, Molly McCabe, Kathryn Echandia-Monroe, Mansi J. Khare, Elise Y. Huang, Sneha Jariwala, Reyna Antilla, Allison Cheney, Alex G. Lee, Leanne C. Sayles, Stanley G. Leung, Yvonne A. Vasquez, Lauren Sanders, David Haussler, Sofie R. Salama, E. Alejandro Sweet-Cordero, Olena M. Vaske

“…To create the compendia, we obtained access to RNA sequence data from repositories containing public data as well as clinical partners with access to non-published data. …”
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Reconstruction of gene regulatory networks from single cell transcriptomic data by M. A. Rybakov, N. A. Omelyanchuk, E. V. Zemlyanskaya

“…This review describes the approaches and programs that are used to reconstruct GRNs from single-cell RNA sequencing (scRNA-seq) data. We consider the advantages of using scRNA-seq data compared to bulk RNA-seq, as well as challenges in GRN inference. …”
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Identification of immune characteristic biomarkers and therapeutic targets in cuproptosis for rheumatoid arthritis by integrated bioinformatics analysis and single-cell RNA sequenc... by Xianbin Li, Xianbin Li, Xianbin Li, Xueli Zhang, Tao Liu, Guodao Zhang, Dan Chen, Suxian Lin

“…Additionally, we investigated the correlation between DE-CRGs and immune infiltration, immune factors, diagnostic efficacy, and potential therapeutic drugs.ResultsLeveraging single-cell RNA sequencing data, we conducted a detailed analysis to elucidate alterations in various cell clusters associated with RA. …”
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Expression of PSMD14 in lung adenocarcinoma and its impact on immune cell infiltration and prognosis: a comprehensive analysis based on RNA and single-cell RNA sequencing by Jing Zhang, Bohao Sun, Jiabin Lai, Weike Kong, Nan Wang, Panyuan Li, Yichen Wu, Zhaochang Jiang

“…A multifaceted approach was adopted, which included the analysis of RNA sequencing (RNA-seq) data, assessment of immune cell infiltration, survival analysis, gene enrichment analysis, and integration of single-cell RNA-seq data to thoroughly evaluate the biological relevance of PSMD14. …”
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Identification of novel metabolism-related biomarkers of Kawasaki disease by integrating single-cell RNA sequencing analysis and machine learning algorithms by Chenhui Feng, Zhimiao Wei, Xiaohui Li, Xiaohui Li

“…Identifying signature cells and genes related to BAM and FAM could offer a deeper understanding of their role in the pathogenesis of KD.MethodWe analyzed the public single-cell RNA sequencing (scRNA-seq) dataset GSE1687323 to characterize the immune cell-type landscape in KD. …”
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Single-Cell Sequencing and Machine Learning Integration to Identify Candidate Biomarkers in Psoriasis: INSIG1 by Zhou X, Ning J, Cai R, Liu J, Yang H, Bai Y

“…In addition, tetrandrine shows promise as a potential treatment for the condition.Keywords: psoriasis, single-cell RNA sequencing, machine learning, INSIG1, pseudotime analysis…”
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A semi-automatic cell type annotation method for single-cell RNA sequencing dataset by Wan Kim, Sung Min Yoon, Sangsoo Kim

“…Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. …”
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Transcriptomics, lipidomics, and single-nucleus RNA sequencing integration: exploring sphingolipids in MASH-HCC progression by Jing Zeng, Grayson Way, Nan Wu, Xixian Jiang, Yun-ling Tai, Derrick Zhao, Lianyong Su, Qianhua Yan, Xuan Wang, Emily C. Gurley, Phillip B. Hylemon, Sayed Obaidullah Aseem, Arun J. Sanyal, Jiangao Fan, Huiping Zhou

“…Total RNA sequencing data, NanoString nCounter® Gene profiling, and single-nucleus RNA sequencing (snRNA-seq) GEO data (GSE225381) were used in characterizing gene regulation in MASH-HCC progression. …”
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Integrated analysis of single-cell, spatial and bulk RNA-sequencing identifies a cell-death signature for predicting the outcomes of head and neck cancer by Yue Pan, Lei Fei, Shihua Wang, Hua Chen, Changqing Jiang, Hong Li, Changsong Wang, Yao Yang, Qinggao Zhang, Yongwen Chen

“…BackgroundCell death plays an essential role in carcinogenesis, but its function in the recurrence and postoperative prognosis of head and neck cancer (HNC), which ranks as the 7th most common malignancy globally, remains unclear.MethodsData from five main subtypes of HNC related single-cell RNA sequencing (scRNA-seq) were recruited to establish a single-cell atlas, and the distribution of cell death models (CDMs) across different tissues as well as cell subtypes were analyzed. …”
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Metabolism-associated marker gene-based predictive model for prognosis, targeted therapy, and immune landscape in ovarian cancer: an integrative analysis of single-cell and bulk RN... by Lele Ling, Bingrong Li, Boliang Ke, Yinjie Hu, Kaiyong Zhang, Siwen Li, Te Liu, Peng Liu, Bimeng Zhang

“…Thus, it is of utmost significance to identify potent prognostic biomarkers and delve into the exploration of novel therapeutic drugs and targets, in pursuit of advancing the treatment of OC. Methods Single-cell RNA sequencing (scRNA-seq) data related to OC were analyzed using AUCell scores to identify subpopulations at the single-cell level. …”
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The cancer stem cells characteristics analysis of LGR5 + cells that influence lung cancer risk by using single cell RNA-seq analysis by Ge Wen, Shaoqing Niu, Shiqi Mei, Senming Wang

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Integrated single-cell analysis reveals the regulatory network of disulfidptosis-related lncRNAs in bladder cancer: constructing a prognostic model and predicting treatment respons... by Jiafu Xiao, Jiafu Xiao, Jiafu Xiao, Wuhao Liu, Wuhao Liu, Wuhao Liu, Jianxin Gong, Jianxin Gong, Jianxin Gong, Weifeng Lai, Weifeng Lai, Weifeng Lai, Neng Luo, Neng Luo, Neng Luo, Yingfan He, Junrong Zou, Junrong Zou, Zhihua He, Zhihua He, Zhihua He

“…This study aims to investigate disulfidptosis-related lncRNAs (DRLs) as potential prognostic markers for BLCA patients.MethodsUtilizing single-cell sequencing data, RNA sequencing data, and corresponding clinical information sourced from the GEO and TCGA databases, this study conducted cell annotation and intercellular communication analyses to identify differentially expressed disulfide death-related genes (DRGs). …”
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Single-cell pseudotime and intercellular communication analysis reveals heterogeneity and immune microenvironment in oral cancer by Hanjun Liu, Lian Xie, Xuemin Xing, Lili Hou, Jinfeng Zhang, Ling Yang

“…Abstract Background Oral cancer is one of the most prevalent malignant neoplasms globally, with its microenvironment being extremely complicated and heterogeneous with regard to distribution of different types of cells, which creates a barrier against treatment. We integrated single-cell RNA sequencing, pseudotime analysis, and intercellular communication to identify subtypes, state transitions, and interactions in the development of oral cancer and their roles in tumor progression and immune response. …”
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Metabolic reprogramming and macrophage expansion define ACPA-negative rheumatoid arthritis: insights from single-cell RNA sequencing by Yafeng Jiang, Zhaolan Hu, Roujie Huang, Kaying Ho, Pengfei Wang, Jin Kang, Jin Kang

“…BackgroundAnti-citrullinated peptide antibodies (ACPA)-negative (ACPA−) rheumatoid arthritis (RA) presents significant diagnostic and therapeutic challenges due to the absence of specific biomarkers, underscoring the need to elucidate its distinctive cellular and metabolic profiles for more targeted interventions.MethodsSingle-cell RNA sequencing data from peripheral blood mononuclear cells (PBMCs) and synovial tissues of patients with ACPA− and ACPA+ RA, as well as healthy controls, were analyzed. …”
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Single-cell RNA sequencing of human double-negative T cells reveals a favorable cellular signature for cancer therapy by Li Zhang, Sergio Rutella, Jongbok Lee, Ismat Khatri, Yoosu Na, Enoch Tin, Karen Fang, Michele Nawata, Juan Arteaga, Mark D Minden

“…Collectively, this hinders our ability to bolster DNT functionalities in cancer therapy. Here, we performed single-cell RNA sequencing with in vitro and in vivo functional analysis on DNTs. …”
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