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Series GSE104782 Query DataSets for GSE104782
Status Public on Jul 20, 2018
Title Single-cell RNA-seq analysis reveals the progression of human osteoarthritis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Understanding the molecular mechanisms underlying human cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). Here, we report the molecular programmes and lineage progression patterns controlling human OA pathogenesis using single-cell RNA sequencing (scRNA-seq). We performed unbiased transcriptome-wide scRNA-seq analysis, computational analysis and histological assays on 1464 chondrocytes from 10 patients with OA undergoing knee arthroplasty surgery. We investigated the relationship between transcriptional programmes of the OA landscape and clinical outcome using severity index analysis and correspondence analysis. We identified seven molecularly defined populations of chondrocytes in human OA cartilage, including three novel phenotypes with distinct functions. We presented gene expression profiles and transcriptional networks among chondrocytes at different OA stages at single-cell resolution. We found a potential transition among proliferative chondrocytes, prehypertrophic chondrocytes and hypertrophic chondrocytes (HTCs) and defined a new subdivision within HTCs. We revealed novel markers for cartilage progenitor cells (CPCs) and demonstrated a relationship between CPCs and fibrocartilage chondrocytes using computational analysis. Notably, we derived predictive targets with respect to clinical outcomes and clarified the role of different cell types for the early diagnosis and treatment of OA.
 
Overall design 34 Samples
 
Contributor(s) Ji Q, Zheng Y, Zhang G, Hu Y, Fan X, Hou Y, Wen L, Li L, Xu Y, Wang Y, Tang F
Citation(s) 30026257
Submission date Oct 10, 2017
Last update date Sep 04, 2019
Contact name Yuxuan Zheng
E-mail(s) zhengyuxuan1994@126.com
Organization name Peking University
Street address Road Yiheyuan
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (34)
GSM2807808 P9 single cell RNA-seq
GSM2807809 P10 single cell RNA-seq
GSM2807810 P11 single cell RNA-seq
Relations
BioProject PRJNA413810
SRA SRP119687

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104782_RAW.tar 21.5 Mb (http)(custom) TAR (of TXT)
GSE104782_Table_Cell_quality_information_and_clustering_information.xlsx 109.7 Kb (ftp)(http) XLSX
GSE104782_all_processed_data_barcode.txt.gz 4.9 Kb (ftp)(http) TXT
GSE104782_allcells_UMI_count.txt.gz 9.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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