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Sample GSM1224752 Query DataSets for GSM1224752
Status Public on Sep 05, 2013
Title c-FostetON Keratinocyte. 6h. Replicate 2.
Sample type RNA
 
Source name Keratinocytes from the tail
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: c-FostetON keratinocytes
treatment: untreated
time: 6h
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 C6h_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

Data table header descriptions
ID_REF
VALUE VST transformed, RSN normalized signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2659724 6.781358227 0.249373434
ILMN_2706226 6.774643153 0.29197995
ILMN_1217123 6.7818051 0.245614035
ILMN_2780205 11.51512216 0
ILMN_2713160 6.676993949 0.95112782
ILMN_2650094 6.763510386 0.401002506
ILMN_2703479 6.753410253 0.486215539
ILMN_2952493 6.795215165 0.154135338
ILMN_2731592 6.790747662 0.179197995
ILMN_2729743 6.83105404 0.022556391
ILMN_1252621 7.789872806 0
ILMN_3162407 10.55545405 0
ILMN_2692952 6.841526816 0.010025063
ILMN_2910076 6.762761597 0.409774436
ILMN_2709047 7.807428463 0
ILMN_2718462 7.069457281 0
ILMN_2882078 7.764717601 0
ILMN_2882079 6.915124746 0
ILMN_2771368 6.752011795 0.498746867
ILMN_2724039 6.767321189 0.363408521

Total number of rows: 25697

Table truncated, full table size 844 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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