NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8279865 Query DataSets for GSM8279865
Status Public on May 22, 2024
Title AMSC_POP#9
Sample type SRA
 
Source name subcutaneous abdominal lipoaspirate
Organism Homo sapiens
Characteristics tissue: subcutaneous abdominal lipoaspirate
cell type: primary adipose derived stromal/stem cells (AMSC or ASC)
treatment: serum free expansion medium supplemented with human Platelet Lysate (hPL)
time: 9-14 days
density of_cultures_cells: confluency
diseases state: pelvic organ prolapse (POP)
Growth protocol Both type of cells (adipose derived stem cells and vaginal fibrobalsts) were expanded in clinically relevant advanced MEM medium (ThermoFisher) supplemented with 5% human platelet lysate (hPL) (PLTMax®, Mill Creek Life Sciences, Rochester, MN), 2U/ml heparin, and 2mM GlutaMAX™ and passaged 2-3 times.
Extracted molecule total RNA
Extraction protocol Confluent ASCs and VFBs cultures were harvested in TRIzol (ThermoFisher). RNA was extracted with Direct-zol RNA kit (Zymo Research). 200 ng of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq mRNA Protocol following manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description JC4
Data processing processed with Mayo Clinic internal secondary pipeline MAPRseq. Basically reads QC by cutadapt, aligned by BWA, mutation called by GATK
FDR <0.05) to identify differentially expressed genes (DEG).
Assembly: HG38
Supplementary files format and content: gene expression profiling (tab-delimited)
Supplementary files format and content: differential gene expression (tab-delimited)
 
Submission date May 20, 2024
Last update date May 22, 2024
Contact name Xianfeng Chen
E-mail(s) chen.xianfeng@mayo.edu
Organization name Mayo Clinic
Street address 13400 E Shea Blvd
City Scottsdale
State/province AZ
ZIP/Postal code 85259
Country USA
 
Platform ID GPL20301
Series (1)
GSE267852 Cell type specific differences in the transcriptomes of adipose derived stem cells and vaginal fibroblasts in patients with pelvic organ prolapse
Relations
BioSample SAMN41323764
SRA SRX24519156

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap