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Sample GSM717688 Query DataSets for GSM717688
Status Public on Jan 24, 2012
Title BT549-T
Sample type RNA
 
Source name BT549 Treated
Organism Homo sapiens
Characteristics treatment: treatment with DAC
Treatment protocol Cells were seeded (2 X l0^5 cells / T75 flasks) for 24h then media were removed and cells were freshly exposed to the 5-aza-2’-deoxycytidine (DAC) (Sigma Chemical Co.) at concentrations of l00nM in suspension culture every 24h until cultured cells reached 80-85 % confluence (~5 days). The cells were split for 10 follow-up passages at “drug holiday” condition.
Growth protocol HB2 cell line was cultured in DMEM, 10% FBS, Insulin (0.01 mg/ml, hydrocortisone (500 ng/ml). MDA-MB231, HS578T and MCF7 cell linee were cultured in DMEM, 10% FBS. SKBR3 cell line was cultured in McCoys 5A, 10% FBS. BT549 cell line was cultured in RPMI medium 1640, 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN AG) according to the manufacturer's instructions. The RNeasy MinElute Cleanup Kit (QIAGEN AG) was used for isolation and purification of enriched miRNAs.
Label biotin
Label protocol Biotinylated microRNAs were prepared according to the FlashTag Biotin HSR RNA Labeling protocol (Genisphere) using 100ng RNA.
 
Hybridization protocol The labelled products were hybridized for 18 hr at 45C on Affymetrix GeneChip miRNA array (v1.0). GeneChips were washed and stained on GeneChip Fluidics 450 Workstations (Affymetrix Inc.).
Scan protocol The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.)
Description MicroRNA expression data directly after treatment with DAC
Data processing The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed miRNAs were defined using Partek Genomics Suite software v6.5 (Partek Incorporated, Missouri, USA) and and RMA normalization.
 
Submission date Apr 29, 2011
Last update date Jan 24, 2012
Contact name Ramin Radpour
Organization name University of Bern
Department Department for BioMedical Research
Street address Murtenstrasse 35
City Bern
ZIP/Postal code 3008
Country Switzerland
 
Platform ID GPL8786
Series (2)
GSE28969 MicroRNA expression data from human breast cancer cell lines after demethylation treatment.
GSE28976 Expression data from human breast cancer cell lines after demethylation treatment

Data table header descriptions
ID_REF
VALUE Signal intensity

Data table
ID_REF VALUE
hsa-let-7a-star_st 1.56275
hsa-let-7a_st 13.3649
hsa-let-7b-star_st 2.84502
hsa-let-7b_st 13.9728
hsa-let-7c-star_st 1.71096
hsa-let-7c_st 12.8567
hsa-let-7d-star_st 3.59388
hsa-let-7d_st 11.9081
hsa-let-7e-star_st 3.62139
hsa-let-7e_st 12.2548
hsa-let-7f-1-star_st 2.00132
hsa-let-7f-2-star_st 2.01991
hsa-let-7f_st 8.70048
hsa-let-7g-star_st 2.5141
hsa-let-7g_st 8.24182
hsa-let-7i-star_st 1.72539
hsa-let-7i_st 11.9856
hsa-miR-100-star_st 1.57106
hsa-miR-100_st 12.5373
hsa-miR-101-star_st 1.5233

Total number of rows: 847

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM717688.CEL.gz 185.4 Kb (ftp)(http) CEL
Processed data included within Sample table

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