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Sample GSM462989 Query DataSets for GSM462989
Status Public on May 21, 2010
Title RA + RA.time + RA.cells + RA.cells.time
Sample type RNA
 
Channel 1
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 Cy5
Label protocol miRNA was labeled by RNA-ligase mediated ligation of Cy dye-coupled dinucleotides.
 
Channel 2
Source name 231_48hr_UT_21
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
time: 48 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 -0.373534442
2 0.217050877
3 -0.123446878
4 -0.059694652
5 0.130314457
6 -0.074960691
7 -0.277139732
8 0.080525491
9 -0.158996493
10 -0.040125694
11 0.011476911
12 -0.034964659
13 -0.193383101
14 -0.253721146
15 0.196784735
16 0.871707228
17 0.033513816
18 0.104618498
19 -0.041824763
20 -0.043978547

Total number of rows: 3072

Table truncated, full table size 51 Kbytes.




Supplementary file Size Download File type/resource
GSM462989_min_015.spot.gz 318.8 Kb (ftp)(http) SPOT
Processed data included within Sample table

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