|
| Status |
Public on Mar 12, 2010 |
| Title |
XX1-K |
| Sample type |
RNA |
| |
|
| Source name |
Kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
gender: female
age: 12 weeks old
genetic background: random bred MF1, one single progenitor X chromosome background
genotype/variation: 40,XX from 40,In(X)1H/XPaf x 40,XY
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from homogenized tissues using Trizol reagent and purified using a column based centrifugation method (Qiagen) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotin-16 UTP of in vitro transcribed RNA. Used Illumina RNA amplification kit (Cat # 1755 Ambion US)
|
| |
|
| Hybridization protocol |
1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 16 hours at 58 degrees celsius. 1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 15 hours at 55 degrees celsius. The microarrays were washed and then stained with streptavidin conjugated to Cy3 fluorescent dye. The staining procedure relies on the affinity of streptavidin to biotin which is incorporated into the UTP residues of the hybridised cRNA sample. Arrays were then washed again and air dried.
|
| Scan protocol |
Microarrays were scanned under 532nm laser illumination using a confocal type image system (BeadArray Reader, Illumina California USA).
|
| Description |
40,XX from 40,In(X)1H/XPaf x 40,XY
|
| Data processing |
The values for each bead in the array were imported into the Illumina software BeadStudio for preliminary quality checks, summarized according to bead type and then exported into R. Normalization across all arrays was performed on a log scale using the quantile normalization method implemented in the Lumi normalization package from the bioconductor repository (www.bioconductor.org).
|
| |
|
| Submission date |
Nov 07, 2008 |
| Last update date |
Aug 04, 2010 |
| Contact name |
Alexandra M. Lopes |
| E-mail(s) |
[email protected]
|
| Organization name |
IPATIMUP
|
| Lab |
Population Genetics
|
| Street address |
R. Dr. Roberto Frias s/n
|
| City |
Porto |
| ZIP/Postal code |
4200-465 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL6105 |
| Series (1) |
| GSE13520 |
Expression profiles of (40,XX) and (39,XO) females |
|
