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Sample GSM1240806 Query DataSets for GSM1240806
Status Public on Oct 01, 2014
Title BM1.replicate4
Sample type RNA
 
Source name BM1.replicate4
Organism Homo sapiens
Characteristics group: BM1
date: 2009feb
progenitor (father): A
progenitor (mother): F
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 11.74461286
1053_at 11.16823327
117_at 6.510671011
121_at 7.376553603
1255_g_at 3.492624683
1294_at 6.611933103
1316_at 6.061355481
1320_at 7.482322076
1405_i_at 3.762107909
1431_at 4.408208295
1438_at 6.404890649
1487_at 9.788067803
1494_f_at 5.106595208
1552256_a_at 8.945629097
1552257_a_at 11.25598639
1552258_at 6.653625816
1552261_at 5.846810486
1552263_at 5.434058691
1552264_a_at 7.922950856
1552266_at 6.366696008

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1240806_AAFeb09--66-2009--BM1B2.CEL.gz 5.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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