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Sample GSM462990 Query DataSets for GSM462990
Status Public on May 21, 2010
Title RA + RA.cells
Sample type RNA
 
Channel 1
Source name 231_6hr_+A_17
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_6hr_UT_13
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
time: 6 hours
protocol: untreated
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 0.007886935
2 0.332615643
3 -0.114886494
4 0.125071394
5 0.087807117
6 -0.01434715
7 0.14850412
8 0.202070873
9 -0.25345796
10 0.233092695
11 0.072631085
12 0.045097394
13 0.047760224
14 -0.227798208
15 -0.116915203
16 0.052642459
17 -0.058286543
18 0.139745006
19 0.015406199
20 0.031167495

Total number of rows: 3072

Table truncated, full table size 51 Kbytes.




Supplementary file Size Download File type/resource
GSM462990_min_016.spot.gz 318.2 Kb (ftp)(http) SPOT
Processed data included within Sample table

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