|
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. |
|