ArticleBioengineered2021
Combining bulk and single-cell RNA-sequencing data to reveal gene expression pattern of chondrocytes in the osteoarthritic knee.
Article in Bioengineered, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 47 citations in OpenAlex.
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- Advances in the pathology and treatment of osteoarthritis.Journal of advanced research · 2025Review
- Whole transcriptome profiling of cardiac injury: insights from a neonatal mouse sepsis model.Genes & genomics · 2025Article
- Gut microbiota and blood biomarkers in IBD-Related arthritis: insights from mendelian randomization.Scientific reports · 2025Article
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- Integrated Single-Cell RNA Sequencing and Proteome-Wide Mendelian Randomization Identifies Therapeutic Targets for Psoriasis and Associated Complications.Psoriasis (Auckland, N.Z.) · 2025Article
- An Update on Emerging Regenerative Medicine Applications: The Use of Extracellular Vesicles and Exosomes for the Management of Chronic Pain.Current pain and headache reports · 2024Review
- Revolutionizing prognostic predictions in colorectal cancer: Macrophage‑driven transcriptional insights from single‑cell RNA sequencing and gene co‑expression network analysis.Oncology letters · 2024Article
- Detection of H1N1 Influenza Virus in the Bile of a Severe Influenza Mouse Model.Influenza and other respiratory viruses · 2024Article
- Multi-modal transcriptomic analysis reveals metabolic dysregulation and immune responses in chronic obstructive pulmonary disease.Scientific reports · 2024Article
- Mesenchymal Stem Cell-Derived Exosomes as a Treatment Option for Osteoarthritis.International journal of molecular sciences · 2024Review
- Integrated single cell-RNA sequencing and Mendelian randomization for ischemic stroke and metabolic syndrome.iScience · 2024Article
- Advancing skeletal health and disease research with single-cell RNA sequencing.Military Medical Research · 2024Review
- Role of crosstalk between synovial cells and chondrocytes in osteoarthritis (Review).Experimental and therapeutic medicine · 2024Review
- Whole-Transcriptome Sequencing of Knee Joint Cartilage from Kashin-Beck Disease and Osteoarthritis Patients.International journal of molecular sciences · 2024Article
- Epigenetics in Knee Osteoarthritis: A 2020-2023 Update Systematic Review.Life (Basel, Switzerland) · 2024Review
- Article
- Causal effects of gut microbiota on sepsis and sepsis-related death: insights from genome-wide Mendelian randomization, single-cell RNA, bulk RNA sequencing, and network pharmacology.Journal of translational medicine · 2024Article
- Single-cell RNA sequencing in osteoarthritis.Cell proliferation · 2023Review
- Probing the communication patterns of different chondrocyte subtypes in osteoarthritis at the single cell level using pattern recognition and manifold learning.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Osteoarthritis (OA) occurs mostly in the knees, hips, finger interphalangeal joints, and spinal facet joints, and is characterized by cartilage degeneration. The existing bulk RNA sequencing (bulk RNA-seq) and single-cell sequencing (scRNA-seq) data for chondrocytes in the osteoarthritic knee joint provide the expression profiles of entire cell populations and individual cells, respectively. Here, we aimed to analyze these two types of sequencing data in order to obtain a more comprehensive understanding of OA. We compared the analysis results of bulk RNA-seq and scRNA-seq from the dataset GSE114007 and the dataset GSE104782, respectively, and identified the differentially expressed genes (DEGs). Then, we tried to find the key The transcription factor is a more fomal term (TFs) and long non-coding RNA (lncRNA) regulation. We highlighted 271 genes that were simultaneously suggested by these two types of data and provided their possible expression pattern in OA. Among the 271 genes, we identified 14 TFs, and TWIST2, MYBL2, RELA, JUN, KLF4, and PTTG1 could be the key TFs for the 271 genes. We also found that 8 lncRNAs among the 271 genes and the lncRNA regulation between CYTOR and NRP1 could contribute to the pain and vascularization of cartilage in the osteoarthritic knee. In short, our research combined the analysis results of bulk RNA-seq and scRNA-seq data for OA chondrocytes, which will contribute to further elucidation of the molecular mechanisms of OA pathogenesis.[Figure: see text].
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