|
| Status |
Public on Sep 22, 2023 |
| Title |
PrE EV2 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate
cell type: primary epithelial cell
sample type: extracellular vesicles (from epithelial cells)
genotype: WT
treatment: primary cell culture in PrEGM media
|
| Treatment protocol |
Prostate tissue slices, epithelial cells, and stromal cells were grown to 70% confluence and then cultured in EV-free media for two days. Evs were isolated from the cell media by differential ultracentifugation.
|
| Growth protocol |
Patient-derived prostate epithelial cells were maintained in PrEBM media in humidified atmosphere with 5% CO2 at 37C. Patient-derived prostate stromal cells were maintained in MCDB media with 5% FBS and DHT and Fgfb in humidified atmosphere with 5% CO2 at 37C. Patient-derived prostate tissue slices were maintained in PrEBM media in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Primary epithelial cell, stromal cell, and tissue slice RNA was harvested using miRNeasy Mini kit (Qiagen). Primary epithelial cell EV, stromal cell EV, tissue slice EV, and serum EV RNA was harvested using the Serum/Plasma miRNeasy kit (Qiagen). 100 ng of total RNA was used for the construction of cell and tissue sequencing libraries. 5 uL of RNA was used for the construction of cell EV, tissue EV, and serum EV sequencing libraries.
microRNA libraries for smallRNA-seq were prepared using the QIAseq miRNA Library Kit following manufacturer's protocols. Libraries were diluted to 10 nM for sequencing.
smallRNA-seq by HiSeq 4000 single read 100 nucleotides
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
CBpz_exo_CTCAGA
primary sequencing analysis (mapping) TISSUE_CELLS.xlsx
ev_CPM_tmm_normalizedcounts_no_piR.xlsx
ev_no_serum_CPM_tmm_normalizedcounts_no_piR.xlsx
|
| Data processing |
GeneGlobe data analysis center
Reads were trimmed using cutadapt, which removed the 3' adapters and low-quality bases
MicroRNA sequences with less than 16 bp and UMI sequences less than 10 bp were removed
MicroRNAs were mapped to miRBase using bowtie, which allowed up to two mismatches
Assembly: miRBase version 22
Supplementary files format and content: Excel files (CPM_tmm_normalizedcounts)
|
| |
|
| Submission date |
Mar 23, 2023 |
| Last update date |
Sep 22, 2023 |
| Contact name |
Morgan Zenner |
| E-mail(s) |
zenner2@uic.edu
|
| Phone |
8473728777
|
| Organization name |
University of Illinois at Chicago College of Medicine
|
| Department |
Pathology
|
| Lab |
Larisa Nonn
|
| Street address |
909 South Wolcott Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE228062 |
Prostate tissue explant, epithelial cell, stromal cell, and extracellular vesicle microRNA characterization by NGS |
|
| Relations |
| BioSample |
SAMN33872761 |
| SRA |
SRX19758280 |
