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Sample GSM462984 Query DataSets for GSM462984
Status Public on May 21, 2010
Title - time - RA.time - cells.time - RA.cells.time
Sample type RNA
 
Channel 1
Source name 231_6hr_+A_16
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
time: 6 hours
protocol: RA treated
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 RNA was extracted with miRNeasy minikit (Qiagen).
Label Cy5
Label protocol miRNA was labeled by RNA-ligase mediated ligation of Cy dye-coupled dinucleotides.
 
Channel 2
Source name 231_48hr_+A_23
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
time: 48 hours
protocol: RA treated
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 RNA was extracted with miRNeasy minikit (Qiagen).
Label Cy3
Label protocol miRNA was labeled by RNA-ligase mediated ligation of Cy dye-coupled dinucleotides.
 
 
Hybridization protocol hybridysed at Adelaide Microarray Facility http://www.microarray.adelaide.edu.au/
Scan protocol Slides were scanned with a GenePix 4000B Scanner (Axon Instruments)
Description no additional information
Data processing Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Morphological opening background correction was applied to mean spot signal intensities. Analysis was performed in R with LIMMA package of BioConductor. Intensity-dependent global loess normalization was applied and the linear model fitted.
VALUE = normalized log2 ratio (Cy5/Cy3)
 
Submission date Oct 19, 2009
Last update date Mar 11, 2010
Contact name Anna Tsykin
E-mail(s) anna.tsykin@adelaide.edu.au
Phone 61 8 8222 3479
Organization name SA Pathology
Department Hanson Institute
Lab Centre for Cancer Research
Street address Frome Road
City Adelaide
State/province SA
ZIP/Postal code 5000
Country Australia
 
Platform ID GPL9472
Series (2)
GSE18628 MicroRNA profiling shows different response to retinoids in estrogen-receptor positive and negative cells
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 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
1 0.829477758
2 -0.012639996
3 -0.314059176
4 0.126318929
5 -0.064516488
6 0.012340325
7 -0.309009707
8 0.147283803
9 -0.439928124
10 -0.083303666
11 0.037088532
12 -0.538828862
13 0.026316341
14 -0.384506552
15 0.000589984
16 0.063614035
17 -0.382085039
18 -0.189373995
19 0.013803485
20 -0.345396774

Total number of rows: 3072

Table truncated, full table size 51 Kbytes.




Supplementary file Size Download File type/resource
GSM462984_min_010.spot.gz 332.3 Kb (ftp)(http) SPOT
Processed data included within Sample table

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