|
| Status |
Public on Dec 01, 2008 |
| Title |
MEF_WT_con_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
WT MEF control
|
| Organism |
Mus musculus |
| Characteristics |
Genotype: HtrA2 wild type, Treatment vehicle 4hrs
|
| Treatment protocol |
MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
|
| Growth protocol |
Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
|
| |
|
| Hybridization protocol |
The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
|
| Description |
Gene expression data from WT MEFs treated for 4hrs with vehicle
|
| Data processing |
Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
|
| |
|
| Submission date |
Oct 03, 2008 |
| Last update date |
Oct 09, 2008 |
| Contact name |
Kristina Klupsch |
| Organization name |
Cancer Research UK
|
| Department |
London Research Institute
|
| Lab |
Signal Transduction Laboratory
|
| Street address |
44 Lincoln's Inn Fields
|
| City |
London |
| ZIP/Postal code |
WC2A 3PX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL339 |
| Series (2) |
| GSE13034 |
Differentially regulated genes in HtrA2 knockout MEFs upon rotenone treatment |
| GSE13035 |
Mitochondrial dysfunction by loss of HtrA2 results in the activation of a brain-specific transcriptional stress response |
|
