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Sample GSM1128391 Query DataSets for GSM1128391
Status Public on Aug 28, 2020
Title ROSE RAS transformed FRA1 silenced rep1
Sample type RNA
 
Source name rat ovarian surface epithelium RAS transformed FRA1 silenced
Organism Rattus norvegicus
Characteristics tissue/cell type: ovarian surface epithelium cells
genotype/variation: RAS transformed; FRA1 silenced
Treatment protocol The HRASG12V-transformed human embryonal kidney cells (HA1ER) and their immortalized origin cell line HA1EB were described by [Hahn et al. Nature 400, 464-468 (1999)] . They were cultivated in Minimum Essential Medium Eagle, Alpha Modification (MEM Alpha) from Sigma, supplemented with 10% IFS, 2 mM ultraglutamine, 1% penicillin/streptomycin, 0,1mg/ml hygromycin and 0,5µg/ml puromycin. G418 was freshly added to a final concentration of 0,4 mg/ml . ROSE199, rat ovary epithelial cell line and their KRAS transformed derivative cell line ROSEA25 were described in [Tchernitsa et al. Oncogene 23, 4536-4555 (2004)]. Inducible RAS studies were done in HEK cell line transfected with a constuct bearing Ha-RAS under ER promoter. Cells were treated with tamoxifen before RNA was extracted. U0126 MEK inhibitor was dissolved in DMSO and used in 10µM final concentration for 48h before RNA was extracted.
Growth protocol RAS-ROSE abd ROSE cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) supplemented with 10 % fetal calf serum (FCS) (Sigma-Aldrich), 2 mM Ultraglutamine 1 (Lonza, BioWhittaker), and 100 units/ml penicillin/streptomycin (Biochrom AG) (standard medium). The medium was supplemented with G418 (400 μg/μl). 45000 RAS-ROSE cells were seeded into 6-well plates (BD Falcon) in standard medium 24 h prior to transient transfection of siRNA.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cell lines using the mirVanaTM miRNA Isolation Kit from Ambion® (Austin, TX, USA) according to the manufacturer’s instructions. In order to avoid cross-labeling of premature miRNA we used the gel purification option. Subsequently the quality of the small RNA fraction was controlled on a 15% PAAG gel stained with ethidium bromide.
Label biotin
Label protocol Standard Affymetrix labeling protocol
 
Hybridization protocol Standard Affymetrix hybridization protocol
Scan protocol Standard Affymetrix scanning protocol
Description SAMPLE 12
replicate 1
Data processing The data were normalised using RMA normalisation affy package (v.1.32.1) in R/Bioconductor (v.2.14.1).
 
Submission date Apr 23, 2013
Last update date Aug 28, 2020
Contact name Wasco Wruck
E-mail(s) wasco.wruck@med.uni-duesseldorf.de
Organization name Universitätsklinikum Düsseldorf
Street address Moorenstr. 5
City Düsseldorf
ZIP/Postal code 40225
Country Germany
 
Platform ID GPL1355
Series (2)
GSE46301 A conserved microRNA signature related to cellular transformation by the RAS oncogene (Affymetrix mRNA)
GSE46806 A conserved microRNA signature related to cellular transformation by the RAS oncogene

Data table header descriptions
ID_REF
VALUE log2 RMA normalized
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
1367452_at 12.0832116 P
1367453_at 11.55333211 P
1367454_at 10.60336203 P
1367455_at 12.40128197 P
1367456_at 12.20494644 P
1367457_at 10.48929299 P
1367458_at 8.411621967 P
1367459_at 12.67572383 P
1367460_at 12.54796812 P
1367461_at 11.22254391 P
1367462_at 11.73386168 P
1367463_at 11.89130569 P
1367464_at 10.86125891 P
1367465_at 10.76941743 P
1367466_at 10.30391909 P
1367467_at 10.33930984 P
1367468_at 9.264445666 P
1367469_at 13.08593743 P
1367470_at 10.79670657 P
1367471_at 9.693253212 P

Total number of rows: 31099

Table truncated, full table size 759 Kbytes.




Supplementary file Size Download File type/resource
GSM1128391_A25siFra_1.CEL.gz 2.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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