|
| Status |
Public on Dec 22, 2010 |
| Title |
C57BL/6J Oct4-EGFP+ cells_3 |
| Sample type |
RNA |
| |
|
| Source name |
germ cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
developmental stage: embryo
age: E14.5
gender: XY
tissue: embryonic male gonads
cell type: germ cells
testicular teratoma susceptibility: resistant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from Oct4-EGFP+ sorted germ cell populations (C57BL/6J n=3, 129/SvJ n=2) using the RNeasy Micro kit (Qiagen #74004) with on-column DNase digestion according to manufacturer’s protocols.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was reverse transcribed to cDNA and then transcribed in vitro into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion #AMIL1791) according to manufacturer’s protocols.
|
| |
|
| Hybridization protocol |
750ng of biotin-labelled cRNA was hybridized to MouseRef-8 v2.0 Expression BeadChips (Illumina BD-202-0202) according to Illumina protocols.
|
| Scan protocol |
BeadChips were scanned on the iScan BeadArray Reader (Illumina) following Illumina protocols.
|
| Description |
B6-3
|
| Data processing |
Raw probe level data was imported into GenomeStudio (Illumina) software, average normalized, and the background signal level was subtracted out. Genes that were not detected in at least one sample (detection p-value cutoff = 0.05) were removed from the analysis. The Illumina custom error model with false discovery rate (FDR) correction was applied to detect genes that were differentially expressed between strains. Expression differences were considered significant if the calculated Diffscore was ± 13 (equivalent to a p-value < 0.05).
|
| |
|
| Submission date |
Sep 24, 2010 |
| Last update date |
Dec 22, 2010 |
| Contact name |
Steven C Munger |
| E-mail(s) |
steven.munger@jax.org
|
| Organization name |
The Jackson Laboratory
|
| Lab |
Steven Munger
|
| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE24340 |
Regulation of male germ cell cycle arrest and differentiation by DND1 is modulated by genetic background |
|
