|
| Status |
Public on Dec 31, 2011 |
| Title |
3xTg-HIP-AMI-3 |
| Sample type |
RNA |
| |
|
| Source name |
Hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus
gender: male
genotype/variation: 3xTgAD
age: 18 months
|
| Treatment protocol |
Male 3xTgAD mice, 14 months of age, were maintained on a 12hr light dark cycle in pathogen free conditions. Animals received food and water ad libitum. The test group received 100ug/g body weight amitriptyline-hydrochloride per os in their drinking water (Sigma-Aldrich, St. Louis MO) for 4 months.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA purification was done using glass bead disruption followed by the RNEasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. The RNA was examined for quantity and quality using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
|
| Label |
Streptavidin-Cy3 bound to biotin-labeled cRNA.
|
| Label protocol |
standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
|
| |
|
| Hybridization protocol |
standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's SentrixMouse Ref-8,v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.
|
| Scan protocol |
Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
|
| Description |
= Hippocampus from male 3xTgAD mice, 18 months of age,
|
| Data processing |
Data was extracted using the Illumina BeadStudio software(v3.4). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection p-values is included in the supplemental file.
|
| |
|
| Submission date |
Jan 24, 2011 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE26836 |
Amitriptyline-mediated cognitive enhancement in aged 3xTg Alzheimer’s disease mice is associated with neurogenesis and neurotrophic activity |
|
