|
| Status |
Public on Jul 23, 2014 |
| Title |
Ts1Cje P1 hippocampus biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Ts1Cje P1 hippocampus biological replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
gender: Female
strain: Ts1Cje (Trisomic)
age: P1
tissue: Hippocampus
|
| Treatment protocol |
N/A
|
| Growth protocol |
All sex matched disomic and trisomic littermates involved in the study were generated by mating Ts1Cje males with C57BL/6 female mice. All mice were kept in a controlled environment of equal light/dark cycle. Unlimited standard pellet diet and water were provided. Genomic DNA was extracted from mouse-tails and genotyped using multiplex PCR primers for neomycin and Grik1 (as an internal control) as described previously (Sago et al., PNA, 95(11): 6256-6261).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Qiagen Rneasy micro kit according to the manufacturer's instructions with a Dnase I digestion step.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Labelled RNA samples were hybridised onto Affymetrix GeneChip Mouse Genome 430 2.0 Arrays according to the AGRFs protocol. Samples were prepared for hybridisation to the GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that included 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a GeneChip. The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm. After hybridisation the chip was washed and stained with SAPE using the appropriate fluidics script in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Genechips were scanned using a GeneChip scanner 3000 with the scanner operating software, GCOS.
|
| Data processing |
Normalization with gcRMA using the full (fast=FALSE) algorithm.
|
| |
|
| Submission date |
Jul 19, 2013 |
| Last update date |
Jul 23, 2014 |
| Contact name |
King Hwa Ling |
| E-mail(s) |
lkh@upm.edu.my
|
| Phone |
+603-89472564
|
| Organization name |
Universiti Putra Malaysia
|
| Department |
Department of Biomedical Science
|
| Lab |
NeuroBiology and Genetics Group
|
| Street address |
Faculty of Medicine and Health Sciences
|
| City |
UPM Serdang |
| State/province |
Selangor |
| ZIP/Postal code |
43400 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE49050 |
Expression data from postnatal mouse brain regions of Ts1Cje and disomic C57BL/6 mice. |
|
