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Sample GSM1038220 Query DataSets for GSM1038220
Status Public on Jul 05, 2013
Title AdERbetasiERalphaE2 rep1
Sample type RNA
Source name MCF-7 cells
Organism Homo sapiens
Characteristics cell line: MCF-7
cell type: breast adenocarcinoma
infected with: adenovirus carrying estrogen receptor beta (AdERb)
transfected with: siERalpha
treated with: 10 nM E2 (Sigma-Aldrich) for 24h
Treatment protocol MCF-7 cells expressing endogenous ERalpha were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 50. ERβ only cells were generated from these cells by knockdown of ERα in parental cells using the following siERα sequences from Dharmacon: forward, 5’-UCAUCGCAUUCCUUGCAAAdTdT-3’, and reverse, 5’-UUUGCAAGGAAUGCGAUGAdTdT-3’. siRNA experiments were performed as previously described, and resulted in knocknown of ERα mRNA and protein by greater than 95% (Chang et al, 2008). Briefly, cells were transfected with 20 nM siCtrl or siERα for 48 h after infection. Then cells were treated with 0.1% EtOH (Veh) or 10 nM E2 (Sigma-Aldrich) for 24h. All experiments were conducted with two or more replicates.
Growth protocol MCF-7 cells were maintained in MEM media with 5% Calf serum
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS 3000.
Description Gene expression data from MCF-7 cells, AdenoERbeta infection 72h, siERalpha treatment 24h, 10 nM E2 for 24h
Data processing The data were analyzed with GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Submission date Nov 16, 2012
Last update date Aug 19, 2014
Contact name Zeynep Madak Erdogan
Organization name UIUC
Department FSHN
Lab Zeynep Madak Erdogan
Street address 1201 S Goodwin Ave
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
Platform ID GPL571
Series (2)
GSE42347 Integrative genomics of gene and metabolic regulation by estrogen receptors α and β and coregulators [expression]
GSE42349 Integrative genomics of gene regulation by estrogen receptors and and coregulators

Data table header descriptions
VALUE normalized

Data table
1007_s_at 9.315647109
1053_at 5.184040411
117_at 2.357223993
121_at 2.765825689
1255_g_at 2.333277078
1294_at 2.333277078
1316_at 2.339886066
1320_at 2.333277078
1405_i_at 2.333277078
1431_at 2.333277078
1438_at 2.51889735
1487_at 5.487897226
1494_f_at 2.394936096
1598_g_at 2.333277078
160020_at 2.368765775
1729_at 4.635541604
177_at 2.333277078
1773_at 2.333277078
179_at 2.447528372
1861_at 2.815911193

Total number of rows: 22277

Table truncated, full table size 497 Kbytes.

Supplementary file Size Download File type/resource
GSM1038220_4892.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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