|
| Status |
Public on Feb 02, 2012 |
| Title |
ADAR2_ko expression array |
| Sample type |
RNA |
| |
|
| Source name |
E11.5 femal mouse embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryo
developmental stage: E11.5
strain: ADAR2-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Female mouse embryos were dissected on E11.5, homogenized and total RNA was extracted using peqGOLD TriFast reagent according to manufacturer´s instructions(PEQLAB Biotechnologie GmbH, Erlangen, Germany).
|
| Label |
Cy3
|
| Label protocol |
For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).
|
| |
|
| Hybridization protocol |
The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.
|
| Scan protocol |
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).
|
| Description |
US22502695_252800511444_S01_GE1_105_Jan09_1_3
|
| Data processing |
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).
|
| |
|
| Submission date |
Jan 19, 2012 |
| Last update date |
Feb 02, 2012 |
| Contact name |
Stefanie Tauber |
| E-mail(s) |
stefanie.tauber@univie.ac.at
|
| Organization name |
MFPL
|
| Department |
CIBIV
|
| Street address |
Dr. Bohr-Gasse 9
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13912 |
| Series (1) |
| GSE34626 |
Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs |
|
