|
| Status |
Public on Oct 01, 2010 |
| Title |
kidney_ethanol_rep6 |
| Sample type |
RNA |
| |
|
| Source name |
kidney, ethanol-exposed
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: male
age: postnatal day 28
tissue: kidney
|
| Treatment protocol |
Maternal ad libitum ingestion of 10% (v/v) ethanol from fertilization to GD 8.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the QIAGEN Rneasy-Plus kit in accordance with the prescribed protocol. All RNA samples were checked on Agilent’s Bioanalyzer (Agilent RNA 6000 Nano) and had RNA Integrity Numbers (RINs) of 8-9.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared using the TargetAmp Nano-g Biotin-aRNA Labeling kit for the Illumina system (EPICENTRE Biotechnologies)
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
replicate 6
|
| Data processing |
The dataset was initially analyzed using Illumina's GenomeStudio software and then subjected to additional filtering. Briefly, data normalization and establishment of differential expression using GenomeStudio was performed according to the recommendations of the manufacturer. After normalization based on rank invariant genes, samples were grouped according to treatment into a cohort of offspring of mothers treated with ethanol (ethanol group) and a cohort of offspring of untreated control mothers (control group). Comparing the two groups a confidence value (p value) was then calculated for each probe using the Illumina Custom algorithm. Probes with an unadjusted p-value <0.01 were selected and the resulting datasets were then subjected to the following filtering process: 1) only probes with a ‘detection p-value’ <0.05 in at least one treatment group as determined by the GenomeStudio software and an average signal intensity of >100 in at least one treatment group were included and 2) probes with a change in intensity values above 1.5 fold and below 0.8 fold between the ethanol and control groups were selected.
|
| |
|
| Submission date |
Jul 23, 2010 |
| Last update date |
Oct 01, 2010 |
| Contact name |
Suyinn Chong |
| Organization name |
Queensland Institute of Medical Research
|
| Department |
Division of Genetics and Population Health
|
| Lab |
Epigenetics Laboratory
|
| Street address |
300 Herston Rd
|
| City |
Herston |
| State/province |
Queensland |
| ZIP/Postal code |
4006 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6887 |
| Series (2) |
| GSE23105 |
Postnatal Growth Restriction and Gene Expression Changes in a Mouse Model of Fetal Alcohol Syndrome (Kidney) |
| GSE23115 |
Postnatal Growth Restriction and Gene Expression Changes in a Mouse Model of Fetal Alcohol Syndrome |
|
