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Sample GSM462979 Query DataSets for GSM462979
Status Public on May 21, 2010
Title time + RA.time
Sample type RNA
 
Channel 1
Source name MCF7_48hr_+A_11
Organism Homo sapiens
Characteristics cell line: MCF-7
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 Cy5
Label protocol miRNA was labeled by RNA-ligase mediated ligation of Cy dye-coupled dinucleotides.
 
Channel 2
Source name MCF7_6hr_+A_5
Organism Homo sapiens
Characteristics cell line: MCF-7
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 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 -0.35492767
2 -0.252756739
3 -0.510402511
4 -0.17591631
5 -0.069647719
6 -0.213989262
7 -0.148091042
8 0.246801018
9 -0.093314719
10 0.094745961
11 0.319826139
12 -0.048398218
13 -0.452556
14 -0.039861405
15 -0.268964555
16 -0.038087046
17 -0.270106219
18 -0.240238052
19 -0.186085633
20 0.020958717

Total number of rows: 3072

Table truncated, full table size 51 Kbytes.




Supplementary file Size Download File type/resource
GSM462979_min_005.spot.gz 333.5 Kb (ftp)(http) SPOT
Processed data included within Sample table

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