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Sample GSM458611 Query DataSets for GSM458611
Status Public on May 21, 2010
Title MCF7 cells, retinoic acid effect, time 48h, repl2
Sample type RNA
 
Channel 1
Source name MCF7 cells, retinoic acid treated, time 48h, repl2
Organism Homo sapiens
Characteristics cell line: MCF7
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 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 MCF7 cells, untreated, time 48h, repl2
Organism Homo sapiens
Characteristics cell line: MCF7
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 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 2 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 -0.007049395
13 -0.267310075
14 -0.239903562
15 -0.363904372
16 -0.271923369
17 -0.774712998
18 -0.346176923
19 0.749748263
20 -0.295097662
21 -0.164607434
22 -0.089035825
23 0.046619664
24 0.18017703
25 -0.062692007
26 -0.14707559
27 -0.004000047
28 -0.077184024
29 -0.08345841
30 -0.048258667
31 -0.95254809

Total number of rows: 43376

Table truncated, full table size 762 Kbytes.




Supplementary file Size Download File type/resource
GSM458611.txt.gz 13.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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