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Sample GSM1240797 Query DataSets for GSM1240797
Status Public on Oct 01, 2014
Title Parental.replicate1
Sample type RNA
 
Source name Parental.replicate1
Organism Homo sapiens
Characteristics group: P
date: 2008nov
progenitor (father): A
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 11.80307071
1053_at 11.16282646
117_at 6.362613306
121_at 7.214354863
1255_g_at 3.453012496
1294_at 6.61144044
1316_at 5.661067608
1320_at 7.704051617
1405_i_at 3.7570019
1431_at 4.896281944
1438_at 6.501216338
1487_at 10.01937657
1494_f_at 5.208017591
1552256_a_at 9.928183393
1552257_a_at 10.98164584
1552258_at 5.515564684
1552261_at 5.852575525
1552263_at 5.789453101
1552264_a_at 8.652011935
1552266_at 5.812340394

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1240797_AANov08--40-2008--MCF7-PA.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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