|
| Status |
Public on Jul 01, 2011 |
| Title |
2d old FHH untreated male (4160685018_K) |
| Sample type |
RNA |
| |
|
| Source name |
rat kidney
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Fawn-Hooded Hypertensive
age: 2 days
tissue: kidney
gender: male
treatment: Untreated
|
| Treatment protocol |
Fawn-Hooded Hypertensive (FHH) rats were bred. Pregnant female FHH was treated with NO donor molsidomine in drinking water (120 mg/L) two weeks before to four weeks after birth. The offspring were sacrificed at 2d, 2w and 36w/42w (male/female respectively) old. The kidneys were isolated from these rats and subjected to BeadChip Illumina RatRef-12. Molsidomine-treated rats were compared to age- and gender-matched untreated FHH rats.
|
| Growth protocol |
2d old FHH untreated male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Kidneys was homogenized in TRIzol using beadbeater. Then RNA was extracted from Trizol and purified using NucleoSpin® RNA II kit from Macherey-Nagel (cat. #: 740 955). The purified RNA was sent to ServiceXS.com who processed the samples as recommended by Illumina.
|
| Label |
streptavidin-Cy3
|
| Label protocol |
The samples amplified and labeled using Illumina TotalPrep RNA Amplification Kit (Ambion, cat. nr. IL1791).
|
| |
|
| Hybridization protocol |
Signal is developed with streptavidin-Cy3.
|
| Scan protocol |
The BeadChip is scanned with the Illumina BeadArray Reader, which is a two-channel, 0.8 μm resolution confocal laser scanner. During the scan process, the BeadChip barcode is scanned, ensuring effective data management.
|
| Description |
2d-untreated-male
|
| Data processing |
The raw bead files (each file contained about 1 million beads) was reorganized into non-normalized data files using T4Illumina (see www.nephrogenomics.net/UMCUtrecht/Tools/). The data were log2-transformed and quantile normalized using the program FlexArray (see gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e). The statistical program CyberT was used to signify change in gene expression between any two groups (e.g. Molsidomine-vs-Untreated FHH of 2 days old). P<0.05 was considered significant. In our analysis we use Array_Address_ID, instead of ID_Ref, as identities for the genes because they contain more unique probe codes.
|
| |
|
| Submission date |
Mar 07, 2011 |
| Last update date |
Jul 01, 2011 |
| Contact name |
Sebastiaan Wesseling |
| E-mail(s) |
s.wesseling@umcutrecht.nl
|
| Organization name |
University Medical Center Utrecht
|
| Department |
Nephrology & Hypertension
|
| Lab |
Nephrology & Hypertension
|
| Street address |
Heidelberglaan 100
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6101 |
| Series (1) |
| GSE27725 |
Genome-wide analysis of perinatal effect of nitric oxide (NO) donor molsidomine on the kidneys of Fawn-Hooded Hypertensive (FHH) rats at different ages |
|
