|
| Status |
Public on Jul 05, 2023 |
| Title |
UGM, Male rep1 |
| Sample type |
SRA |
| |
|
| Source name |
urogenital sinus mesenchyme
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: urogenital sinus mesenchyme
Sex: male
age: E18
strain: Sprague-Dawley rats (Harlan Laboratories Inc.)
treatment: no treatment
|
| Treatment protocol |
After separation of mesenchymal and epithelial subsets, UGM and SVM were incubated for four hours in DMEM/F12 medium containing 2% ITS and 10nM DHT, while UGE and SVE were incubated in the same medium without the addition of DHT.
|
| Growth protocol |
All animal experiments were performed in accordance with the Animal Welfare Ethical Review Board at Newcastle University or the Institutional Animal Care and Use Committee at Northshore University HealthSystem Research Institute. Embryonic male UGS was micro-dissected from E18 Sprague-Dawley rats (Harlan Laboratories Inc.) and neonatal P0 SVs were isolated from Wistar Han IGS outbred rats (Charles River Laboratories) as described previously (Hepburn et al., 2020; Lawrence et al., 2013).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen RNeasy Micro Kit
Illumina Tru-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
UGM_Male1
|
| Data processing |
Raw reads were cleaned (adpater trimming, quality-trimming, removal of reads less than 50bp) was performed using Fastp toolkit.
Quality trimmed reads were mapped against the indexed ENSEMBL Rnor_6.0 reference genome using STAR3 aligner (v2.7.10a).
STAR derived mapping results and annotation (GTF) file were fed into the Htseq version 0.7.0.
Differential expression analysis was performed with Bioconductor package DESeq2 (version 1.22.2)
Pathway analysis was performed using ClusterProfiler
Assembly: ENSEMBL Rnor_6.0
Supplementary files format and content: Tab delimited text file containing raw counts for each sample
|
| |
|
| Submission date |
Jun 06, 2023 |
| Last update date |
Jul 05, 2023 |
| Contact name |
Nadia Marie Atallah |
| Organization name |
Purdue University
|
| Department |
Center for Cancer Research
|
| Street address |
201 S. University St
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE234252 |
Human prostate organoid generation and the identification of prostate development drivers using inductive rodent tissues |
|
| Relations |
| BioSample |
SAMN35646879 |
| SRA |
SRX20603354 |
