|
| Status |
Public on May 22, 2024 |
| Title |
VFB_Ctrl#1 |
| Sample type |
SRA |
| |
|
| Source name |
Vaginal excised subepithelum
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Vaginal excised subepithelum
cell type: primary vaginal fibroblasts (VFB or VFBs)
treatment: serum free expansion medium supplemented with human Platelet Lysate (hPL)
time: 9-14 days
density of_cultures_cells: confluency
diseases state: controls - without pelvic organ prolapse (CTRL)
|
| 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 |
JC14
|
| 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 |
SAMN41323768 |
| SRA |
SRX24519138 |
