|
| Status |
Public on Sep 05, 2013 |
| Title |
c-FostetON Keratinocyte. 24h. Replicate 1. |
| Sample type |
RNA |
| |
|
| Source name |
Keratinocytes from the tail
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: c-FostetON keratinocytes
treatment: untreated
time: 24h
|
| Treatment protocol |
c-FostetON keratinocytes were cultured in the presence/abscence of 1ug/ml of Doxicycline.
|
| Growth protocol |
Isolation and culture of mouse primary tail keratinocytes was performed as described elsewhere (Zenz et al., 2003). 24h after plating, keratinocyte media was changed to KC-SFM (Gibco). Keratinocytes were cultured at 32ºC. Medium was changed every other day and, if needed, supplemented with Dox at 1μg/L. Cells were collected at different time points after Dox treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol.
|
| Label |
biotin
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
RNA of samples was hybridized to the Illumina MouseRef-8 V2 R3 BeadChip array according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).
|
| Scan protocol |
Microarray scanning was done using a Beadstation array scanner.
|
| Description |
A24h_Fos-dox
|
| Data processing |
Raw data files from the Illumina chip quantification.
Data preprocessing and quality control was conducted using packages of the Bioconductor project implemented in our in-house developed ChipYard framework for microarray data analysis (http://www.dkfz.de/genetics/ChipYard/). In summary microarray probes were annotated based on Ensembl (version 58) using an in house BLAST-based pipeline. Before normalization with variance-stabilizing transformation (VST) and robust spline normalization (RSN) algorithms beads with signals below the negative controls were removed and positive negative and hybridization controls were excluded.
|
| |
|
| Submission date |
Sep 05, 2013 |
| Last update date |
Sep 05, 2013 |
| Contact name |
Marc Zapatka |
| Organization name |
German Cancer Research Center
|
| Department |
B060 Molecular Genetics
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
69120 |
| ZIP/Postal code |
Heidelberg |
| Country |
Germany |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE50621 |
Expression analyses of inducible c-Fos expressing kerationcytes |
|
