|
| Status |
Public on Jan 26, 2016 |
| Title |
PS2APP 13 months SAM14136240 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from whole cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole cortex
genotype: PS2APP
age: 13 months
samid: SAM14136240
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hemicortices were rapidly frozen on dry ice and stored until a full collection was obtained. RNA was extracted using Qiazol per manufacturer instruction's, then cleaned up using RNEasy column with on-column DNase digestion (Qiagen). Quantity and quality of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
|
| Label |
Cy5
|
| Label protocol |
The method for preparation of Cy-dye labeled cRNA and array hybridization was provided by Agilent. Briefly, 1 μg total RNA was converted to double-stranded cDNA and then to Cy5-labeled cRNA using Quick Amp Labeling Kit (Agilent). The labeled cRNA was purified using RNeasy mini kit (Qiagen). cRNA yield and Cy5 incorporation was determined using ND-1000 spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
universal mouse reference (Stratagene)
|
| Organism |
Mus musculus |
| Characteristics |
genotype: NA
age: NA
samid: NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
By vendor
|
| Label |
Cy3
|
| Label protocol |
Method for Cy-dye labeled cRNA preparation was provided by Agilent.
|
| |
|
| |
| Hybridization protocol |
750 ng of labeled cRNA was fragmented and hybridized to Agilent’s Whole Mouse Genome 4x44Kv2 arrays as described in manufacturer’s hybridization kit, against an equal amount of Cy3-labeled universal mouse reference (Stratagene).
|
| Scan protocol |
Following hybridization, microarrays were washed, dried, and scanned on Agilent’s G2505C scanner. Agilent’s Feature Extraction 11.5 software was used to analyze acquired array images.
|
| Description |
PS2APP 13 months SAM14136240
|
| Data processing |
Data were analyzed using the limma package from Bioconductor. ControlType weights were set to 0, spots with background signal more than 50 above the foreground signal were set to the median background intensity, background correction was performed with limma::backgroundCorrect() using the "normexp" method and an offset of 50, limma::normalizeWithinArrays() with the "loess" method, and finally limma::normalizeBetweenArrays() with the "Aquantile" method. This gives the "test" and "reference" normalized probe intensities. Finally, for each probe an "expression ratio" was calculated, the ratio of the normalized signals in the test and reference channels.
|
| |
|
| Submission date |
Nov 13, 2015 |
| Last update date |
Jan 26, 2016 |
| Contact name |
Brad A Friedman |
| E-mail(s) |
[email protected]
|
| Organization name |
Genentech, Inc.
|
| Department |
Bioinformatics
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94133 |
| Country |
USA |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
|
