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Sample GSM1240803 Query DataSets for GSM1240803
Status Public on Oct 01, 2014
Title BM1.replicate3
Sample type RNA
 
Source name BM1.replicate3
Organism Homo sapiens
Characteristics group: BM1
date: 2009feb
progenitor (father): B
progenitor (mother): D
Treatment protocol Cells were grown for 2 days following the growth protocol outlined above and RNA extracted
Growth protocol MCF7 media (Control media): DMEM (Life Technologies), 1X Glutamax (Gibco 35050) and 10% FBS (Biological Industires) when passaging. See growth conditions in Tarragona et al., Journal of Biological Chemistry, 2012), for more details.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies) and quantified using a Nanodrop spectrophotometer. Quality was assessed using a Bioanalyzer (Agilent) and only high quality samples (RIN ≥9) were used for hybridization.
Label biotin
Label protocol 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)
 
Hybridization protocol 3.75 mg cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a Fluidics 450 Station (Affymetrix, Santa Clara, CA). Each sample was hybridized with an Affymetrix Human Genome U133APlus2.0 microarray.
Scan protocol GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)
Description Affymetrix Human Genome U133 Plus 2.0 Array
Data processing Data was quantile normalized and RMA summarized using Bioconductor.
 
Submission date Sep 27, 2013
Last update date Oct 01, 2014
Contact name Evarist Planet Letschert
E-mail(s) evarist.planet@irbbarcelona.org
Organization name IRB Barcelona
Department Biostatistics
Street address C/ Baldiri Reixac 10
City Barcelona
State/province Spain
ZIP/Postal code 08028
Country Spain
 
Platform ID GPL570
Series (2)
GSE51232 Identification of genes associated with bone metastatic breast cancer cells
GSE51238 16q22-24 DNA amplification specifically predicts and mediates, through MAF gene, breast cancer bone metastasis.

Data table header descriptions
ID_REF
VALUE log2 RMA expression estimate

Data table
ID_REF VALUE
1007_s_at 11.85414327
1053_at 10.83474108
117_at 7.265364969
121_at 7.711157475
1255_g_at 3.368525511
1294_at 6.601997742
1316_at 6.395703717
1320_at 7.155880034
1405_i_at 3.641706563
1431_at 5.207365108
1438_at 6.350253456
1487_at 10.06857838
1494_f_at 5.254642426
1552256_a_at 8.809574867
1552257_a_at 11.27316073
1552258_at 6.685634647
1552261_at 6.150551095
1552263_at 5.046297087
1552264_a_at 7.917212549
1552266_at 5.884186197

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1240803_AAFeb09--65-2009--BM1A2.CEL.gz 5.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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