|
| Status |
Public on Dec 20, 2011 |
| Title |
control 1 (saline-treated at P4 and 7) |
| Sample type |
RNA |
| |
|
| Source name |
brain, total RNA from 3 saline-treated males
|
| Organism |
Mus musculus |
| Characteristics |
treatment: ethanol
|
| Treatment protocol |
Mice were injected subcutaneously with 20% ethanol in 0.15M saline (or 0.15M saline alone as a control) at postnatal days 4 and 7. Dosages represented two 2.5 g/kg ethanol doses spaced two hours apart on each day. During treatment, the mother was removed from the cage and replaced following the completion of all injections. To avoid litter effects, mice were sex and weight-matched within litters (ie, control and ethanol-treated mice were parented by the same dam). Mice were weaned at postnatal day 25 and housed in same-sex colonies of 2-4 individuals per cage. At postnatal day 60, mice were sacrificed by CO2 asphyxiation and whole brain tissue were dissected using RNAse-free tools. Brains were snap-frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation.
|
| Growth protocol |
Mice were raised in standard same-sex housing conditions (14/10-hour light/dark cycle, 40-60% humidity,21°C to 24°C temperature). Mice were sacrificed at postnatal day 60.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions and cleaned using RNeasy Mini kit (QIAGEN). RNA quality and quantity was analyzed by Agilent 2100 Bioanalyzer and a NanoDrop ND-1000 spectrophotometer. Equal ug of total brain RNA were pooled from three male mice (from different litters) to minimize litter effect noise.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was synthesized using 200 ng of total RNA using Ambion WE Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays and labelled using the Affymetrix GeneChip WT Terminal Labeling kit.
|
| |
|
| Hybridization protocol |
5.5 ug of single-stranded cDNA was hybridized for 16 hours at 45 degrees C to the array. Liquid handling steps were performed by a GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 using Command Console v1.1
|
| Data processing |
The data were analyzed with Partek Genomics Suite software v6.6. Probes were quantile-normalized using the GeneChip-Robust Multiarray Averaging and log2 transformed. All other settings were left as default.
|
| |
|
| Submission date |
Dec 19, 2011 |
| Last update date |
Dec 20, 2011 |
| Contact name |
Morgan L Kleiber |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Western Ontario
|
| Department |
Biology
|
| Street address |
Biological and Geological Sciences Building
|
| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N6A 5B7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE34549 |
brain expression data from adult mice exposed to ethanol at postnatal day 4 and 7 |
|
