|
| Status |
Public on Dec 31, 2014 |
| Title |
Cumulus Cells, PMSG-Stimulated, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Cumulus Cells, PMSG-Stimulated
|
| Organism |
Mus musculus |
| Characteristics |
cell type: cumulus
pmsg-stimulation: stimulated
|
| Treatment protocol |
Half of the mice were treated with 5 IU equine chorionic gonadotropin 44 hours before isolation of cumulus and mural granulosa cells
|
| Growth protocol |
Fresh samples of cumulus cells and mural granulosa cells were isolated from the ovaries of 22 day old mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturers instructions.
|
| Label |
biotin
|
| Label protocol |
Fragmented biotinylated aRNA were produced from 20ng Total RNA according to the standard protocol using the MessageAmp II aRNA Amplification Kit from Ambion for the first round of amplification and using the MessageAmp II Biotin Enhanced Kit from Ambion for the second round of amplification.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Data processing |
Average signal intensities for each probeset within arrays were calculated by the rma function provided within the affy package for R using a custom (Ensembl Transcript v13) CDF file (Dai et al., 2005; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/version.html). The RMA method incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.
|
| |
|
| Submission date |
Mar 12, 2014 |
| Last update date |
Dec 31, 2014 |
| Contact name |
Timothy Michael Stearns |
| E-mail(s) |
tim.stearns@jax.org
|
| Organization name |
The Jackson Laboratory
|
| Department |
Computational Sciences
|
| Lab |
Statistics
|
| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL18416 |
| Series (1) |
| GSE55845 |
Analysis of transcriptomic diversitification of developing cumulus and mural granulosa cells in mouse ovarian follicles |
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