|
| Status |
Public on Dec 21, 2013 |
| Title |
KD d6 replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
KD d6
|
| Organism |
Mus musculus |
| Characteristics |
cell type: RGC-like NPC
treatment: Zrf1 KD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol
|
| Label |
Cy3
|
| Label protocol |
100 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 LowInputQuick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)
|
| |
|
| Hybridization protocol |
After fragmentation, 600 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 Wash buffer 2 (Agilent).
|
| Scan protocol |
Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT
The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
|
| Data processing |
Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.
|
| |
|
| Submission date |
Dec 20, 2013 |
| Last update date |
Dec 21, 2013 |
| Contact name |
Luciano Di Croce |
| E-mail(s) |
luciano.dicroce@crg.eu
|
| Phone |
+34933160132
|
| Organization name |
Centre for Genomic Regulation
|
| Street address |
Dr. Aiguader, 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13912 |
| Series (2) |
| GSE53541 |
Zrf1 is required to establish and maintain neural progenitor identity (mRNA array) |
| GSE53542 |
Zrf1 is required to establish and maintain neural progenitor identity |
|
