|
| Status |
Public on Oct 30, 2015 |
| Title |
iSSC_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Intermediate spermatogonial stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: intermediate spermatogonial stem cells
age: 3-5 day old
strain: ICR
gender: male
|
| Treatment protocol |
Testicular cell-derived SSCs slowly proliferated and then formed clumplike structures on the somatic cells 2-4 weeks after seeding. Cultured cells were dissociated by trypsinization and re-plated on fresh MEFs every 5-7 days.
|
| Growth protocol |
The enzymatically dissociated testicular cell suspension was plated on 0.1% gelatin-coated dishes (1-1.5 x 10^5 cells/cm2) in serum-free germ stem cell (GS) medium. SSC clumps obtained from early (0-1) and middle (9-10) passages were transferred onto mitomycin-treated mouse embryonic fibroblast (MEF) feeder layers and passaged every 5-6 days. When colonies with a flattened or ES-like shape appeared, they were either continuously cultured in GS medium or transferred into serum-free KSR-mES media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
10ug total RNAs were then amplified and labelled using the Nugen WT Ovation One-Direct RNA Amplification and Nugen FL-Ovation cDNA Biotin Module V2 labelling kits, respectively.
|
| |
|
| Hybridization protocol |
Microarray hybridization was then performed using Affymetrix Mouse Genome 430 2.0 Array.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS 3000 7G scanner .
|
| Description |
Gene expression data from intermediate state SSC
|
| Data processing |
The data were analyzed with robust multi-array average (RMA) method using 'affy' bioconductor package.
|
| |
|
| Submission date |
Oct 19, 2015 |
| Last update date |
Oct 30, 2015 |
| Contact name |
Boyoun Park |
| E-mail(s) |
bypark@yonsei.ac.kr
|
| Organization name |
Yonsei University
|
| Department |
Systems biology
|
| Street address |
50 Yonsei-ro, Seodaemun-gu
|
| City |
Seoul |
| ZIP/Postal code |
120-749 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE74151 |
Expression data from three types of spermatogonial stem cells. |
| GSE74156 |
An integrated systems biology approach identifies positive cofactor 4 as a pluripotency regulatory factor |
|
