|
| Status |
Public on May 01, 2012 |
| Title |
sh JMJD3 + TGFb, replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
sh2 JMJD3 + TGFb
|
| Organism |
Mus musculus |
| Characteristics |
cell type: neural stem cells
knockdown: sh2 JMJD3
treatment: TGFb
age: E12.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol
|
| Label |
Cy3
|
| Label protocol |
500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)
|
| |
|
| Hybridization protocol |
After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).
|
| Scan protocol |
Scanned on an Agilent G2539A scanner at 5um resolution and 110%PMT
The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
|
| Description |
dissected out from embrionic cerebral cortex (E12.5). Cells are stably transfected with a JMJD3 shRNA.
|
| Data processing |
Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.
|
| |
|
| Submission date |
Jan 26, 2012 |
| Last update date |
May 01, 2012 |
| Contact name |
Conchi EI |
| Organization name |
IBMB
|
| Street address |
Baldiri Reixac 15
|
| City |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10333 |
| Series (1) |
| GSE35361 |
JMJD3 is needed to regulate TGF beta responsive genes. |
|
