|
| Status |
Public on Dec 22, 2014 |
| Title |
20.1-20.1 |
| Sample type |
RNA |
| |
|
| Source name |
Brain, left hemisphere excluding cerebellum, 30min asphyxia on E17, E21
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
gender: male
tissue: brain (left hemisphere excluding cerebellum)
developmental stage: E21
experimental group: FA
|
| Biomaterial provider |
Charles River
|
| Treatment protocol |
RNAlater was added directly after excision of the material, and then the material was snap frozen and stored at -80degrees Celsius.
|
| Growth protocol |
Dams were given standard rodent food ad libitum. Pups were cared for by foster dams.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy mini kit, protocol available from www.qiagen.com
|
| Label |
biotin
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double-stranded cDNA in a reverse transcription reaction. Next, the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single-stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.
|
| |
|
| Hybridization protocol |
A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Rat Gene 1.0 ST Arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer's procedures.
|
| Scan protocol |
To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
|
| Data processing |
Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.
|
| |
|
| Submission date |
Dec 03, 2012 |
| Last update date |
Dec 22, 2014 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE42676 |
Functional genomics in perinatal asphyxia and fetal asphyctic preconditioning in the brain |
|
