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Sample GSM458614 Query DataSets for GSM458614
Status Public on May 21, 2010
Title MDA-MB-231 cells, retinoic acid effect, time 48h, repl1
Sample type RNA
 
Channel 1
Source name MDA-MB-231 cells, untreated, time 48h, repl1
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
treatment: Vehicle
time: 48 hours
Treatment protocol logarithmically growing cells were cultured in the presence or absence of 1 micromolar all-trans retinoic acid for 6 or 48 hours. At the end of the experiment total RNA, containing the microRNA fraction, was extracted and used for miR and GX profiling
Growth protocol Cells were grown in F12 medium containing 5% charcoal stripped fetal bovine serum (lonza) containing 10 nM beta-estradiol
Extracted molecule total RNA
Extraction protocol total RNA extracted using Qiagen miRNeasy kit, followed by Rneasy MinElute Cleanup, following manufacturer's instructions
Label Cy5
Label protocol Amino Allyl cDNA Labeling Kit (cat 1705, Ambion), following manufacturer's instructions. Samples were then diluted 1:10 and 15 picomoles of each dye were used for hyhbridization
 
Channel 2
Source name MDA-MB-231 cells, retinoic acid treated, time 48h, repl1
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
treatment: 1 microM Retinoic Acid
time: 48 hours
Treatment protocol logarithmically growing cells were cultured in the presence or absence of 1 micromolar all-trans retinoic acid for 6 or 48 hours. At the end of the experiment total RNA, containing the microRNA fraction, was extracted and used for miR and GX profiling
Growth protocol Cells were grown in F12 medium containing 5% charcoal stripped fetal bovine serum (lonza) containing 10 nM beta-estradiol
Extracted molecule total RNA
Extraction protocol total RNA extracted using Qiagen miRNeasy kit, followed by Rneasy MinElute Cleanup, following manufacturer's instructions
Label Cy3
Label protocol Amino Allyl cDNA Labeling Kit (cat 1705, Ambion), following manufacturer's instructions. Samples were then diluted 1:10 and 15 picomoles of each dye were used for hyhbridization
 
 
Hybridization protocol hybridization and washing were done according to Agilent protocol (GE version 5.5 )
Scan protocol Agilent Technologies Scanner G2505B US45102933, 5 micron resolution and XDR protocol, using the Agilent scan control software.
Description Biological replicates 1 of 2
Data processing Image data analysis was performed using the Feature extraction software (v9.1). The raw data FE files report log10 (Cy5/Cy3) ratios. Detailed description of the protocols used is reported in each raw data file. LogRatios are derived by Lowess normalizatin of Median Signals (maNorm function of marray package in Bioconductor).
 
Submission date Oct 02, 2009
Last update date Mar 11, 2010
Contact name Maddalena Fratelli
E-mail(s) maddalena@marionegri.it
Phone +390239014217
Organization name "Mario Negri" Institute
Lab Molecular Biology
Street address Via La Masa, 19
City Milano
ZIP/Postal code I20156
Country Italy
 
Platform ID GPL4133
Series (2)
GSE18390 Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA profiling
GSE18693 Effects of retinoids on estrogen-receptor-positive and -negative breast carcinoma cells: mRNA and miRNA profiling

Data table header descriptions
ID_REF
VALUE normalized log2 (Cy5/Cy3) ratio

Data table
ID_REF VALUE
12 0.171542007
13 -0.81430332
14 -0.240687752
15 -0.214506221
16 -0.346114284
17 -0.340030049
18 -0.259199657
19 0.63517812
20 -0.887917916
21 -0.088762808
22 0.050202573
23 -0.110623521
24 0.288973987
25 -0.134344975
26 -0.24393038
27 0.261291144
28 0.161415117
29 -0.196137138
30 -0.047914808
31 -0.656420229

Total number of rows: 43376

Table truncated, full table size 764 Kbytes.




Supplementary file Size Download File type/resource
GSM458614.txt.gz 13.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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