|
| Status |
Public on Feb 28, 2014 |
| Title |
mPFC_virgin_rep5 |
| Sample type |
RNA |
| |
|
| Source name |
virgin adult female_medial prefrontal cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: Outbred hsd:ICR
maternal state: virgin
tissue: microdissected medial prefrontal cortex
|
| Treatment protocol |
On postpartum day 0, pups were culled, if necessary, to standardize litter size to 11. Tissue was collected on postpartum day 7.
|
| Growth protocol |
The strain of mice used was outbred hsd:ICR mice purchased from Harlan labs (Madison, WI). Maternal were housed with a breeder male for two weeks while virgin mice were co-housed with two other female mice for the same time period. After the mating period, all females from both groups were individually housed through parturition until tissue collection (postpartum day 7). Each virgin control sample was collected on the same day as a postpartum day 7 maternal sample.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad, Hercules, CA, USA), which uses a guanidinium thiocyanate-phenol-chloroform extraction followed by a spin column cleanup and purification. RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was assessed using an RNA Pico Chip on an Agilent BioAnalyzer 2100.
|
| Label |
Biotin
|
| Label protocol |
200ng of each total RNA sample were labeled with an Ambion GeneChip WT Expression Kit (Ambion, Austin, TX, USA) according to the manufacturer's specifications.
|
| |
|
| Hybridization protocol |
Samples were hybridized to arrays at 45 degrees C for 16 hours following procedures outlined in the GeneChip WT Terminal Labeling and Hybridization Use Manual , Rev. 4.
|
| Scan protocol |
Arrays were scanned on the Affymetrix GC3000 G7 scanner, and data were extracted and processed using Affymetrix Command Console v3.1.1.1229.
|
| Description |
Vir5
|
| Data processing |
Raw array data were normalized and summarized at the probeset level using Affymetrix Power Tools v1.12.0 with default settings for PLIER with GC-bin background correction. Summarized data were analyzed using limma for BioConductor v3.6.9
|
| |
|
| Submission date |
Jan 27, 2014 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Xinyu Zhao |
| E-mail(s) |
xinyu.zhao@wisc.edu
|
| Phone |
6082639906
|
| Organization name |
University of Wisconsin Madison
|
| Street address |
1500 HIghland Ave, Wiasman Center North Tower T513
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE54426 |
Medial prefrontal cortex: genes linked to bipolar disorder and schizophrenia have altered expression in the highly social maternal phenotype |
|
