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| Status |
Public on Sep 13, 2024 |
| Title |
Chondrocytes differentiation and immune cells interactions of Endplate Cells in Human Intervertebral Disc Degeneration |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We performed the single-cell RNA-sequencing analysis (scRNA-seq) of the cells focusing on degenerative human endplates. By unsupervised clustering of the 8,534 single-cell based on the gene expression, we identified nine distinct cell types. We employed Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis, and the single-cell regulatory network inference and clustering (SCENIC) to determine the enriched pathways and transcriptional activities across seven chondrocyte subpopulations. Furthermore, two cell fates of chondrocyte differentiation were found by trajectory analysis, one was enriched in inflammation-related genes, and the other was related to extracellular matrix (ECM). Additionally, the intercellular interactions of MAs and chondrocytes, T/NK cells and chondrocytes were examined by ligand-receptor pairs analysis, showing the important regulative function of FN1 from MAs and CD74 from T/NK cells during endplate degeneration.
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| Overall design |
Cartilage endplate tissue was obtained from two patients diagnosed with modic changes at the levels of L3-L4 or L4-L5, who were undergoing surgery for disc herniation, and analyzed using scRNA-seq. The patients were a 58-year-old female and a 66-year-old male, respectively. All participants included were confirmed with MRI images before surgery.
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| Web link |
https://www.nature.com/articles/s41598-024-71891-5#citeas
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| Contributor(s) |
Shi C, Ni S, Fan Y, Huang X |
| Citation(s) |
39271714 |
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| Submission date |
Feb 14, 2024 |
| Last update date |
Sep 15, 2024 |
| Contact name |
Chenhao Shi |
| E-mail(s) |
chenhaoshi@yeah.net
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| Organization name |
The first affiliated hospital of Zhengzhou university
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| Street address |
No.1 Jianshe Dong Road, Erqi District, 450052, Zhengzhou, Henan, China
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| City |
Zhengzhou |
| State/province |
He'nan |
| ZIP/Postal code |
450052 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA1076495 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE255768_RAW.tar |
46.0 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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