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Series GSE267852 Query DataSets for GSE267852
Status Public on May 22, 2024
Title Cell type specific differences in the transcriptomes of adipose derived stem cells and vaginal fibroblasts in patients with pelvic organ prolapse
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The purpose of the study was to understand the molecular phenotypes of adipose-derived stem cells (ASCs) and vaginal fibroblasts (VFBs) and whether pelvic organ prolapse (POP) affects their biological properties. We performed RNA sequencing of paired ASCs and VFBs from six patients with POP and six controls (CTRL). We found no differentially expressed genes (DEG) between POP and CTRL in ASCs and VFBs. Less stringent statistical analysis of VFBs transcriptome showed 23 genes with higher and 29 genes with 2-fold lower expression in POP compared to CTRL. Among the latter were five genes involved in the synaptogenesis pathway found to be significant. We were only able to validate POP related differences for VLDLR protein. We found 508 DEG with 4-fold difference between ASCs and VFBs (when POP and CTRL samples were combined for each cell type). The DEG with higher expression in each cell type formed distinct functional networks including Homeobox transcription factors, extracellular matrix (ECM) related proteins, growth factors, and others. These data show that cell-specific RNA populations are intrinsically more characteristic than the disease peculiarities and that VLDLR may play a role in POP pathogenesis.
Overall design The transcriptomes of POP and CTRL in either ASCs or VFBs were compared (DESeq2, FDR <0.05) to identify differentially expressed genes (DEG). Subsequently, the transcriptomes of VFBs were compared between POP and CTRL (non-adjusted p <0.01; 2-fold difference in gene expression) followed by Ingenuity Pathway Analysis on DEG considering that pathways with FDR <0.05 might be pathogenic. The identified DEG were validated at a protein level by immunoblotting. We also performed a pairwise comparison after combining the gene expression data of POP and CTRL for ASCs and VFBs to identify cell type specific DEG and analyzed the functional associations among them (STRING platform).
Contributor(s) Yourka T, Xianfeng C
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BioProject PRJNA1110204
Submission date May 20, 2024
Last update date May 22, 2024
Contact name Xianfeng Chen
Organization name Mayo Clinic
Street address 13400 E Shea Blvd
City Scottsdale
State/province AZ
ZIP/Postal code 85259
Country USA
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (24)
GSM8279857 AMSC_Ctrl#1
GSM8279858 AMSC_Ctrl#2
GSM8279859 AMSC_Ctrl#3

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

Supplementary file Size Download File type/resource
GSE267852_ASC3.vs.VFB3vs2_1st.worksheet.with.all.genes.txt.gz 1.7 Mb (ftp)(http) TXT
GSE267852_ASCvVFB_heatmap_for_metadata_submission_to_GEO.xlsx 980.9 Kb (ftp)(http) XLSX
GSE267852_PRJNA1110204.merged_gene_count.tsv.gz 2.3 Mb (ftp)(http) TSV
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