|
| Status |
Public on Oct 21, 2011 |
| Title |
IDC28 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from breast tumor biopsies
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
cell type: infiltrative breast ductal carcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1mg of total RNA from each independent tumours were labelled with Cy5-dUTP and as control a pooled RNA obtained from equal concentration of each RNA tumor sample labelled with Cy3-dUTP was used. The amplification and labelling of mRNA were performed using Low RNA Linear Amplification Kit (Agilent technologies), following manufacturer’s protocol
|
| Label |
Cy5
|
| Label protocol |
1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
Pool from the analysed samples
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
cell type: infiltrative breast ductal carcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1mg of total RNA from each independent tumours were labelled with Cy5-dUTP and as control a pooled RNA obtained from equal concentration of each RNA tumor sample labelled with Cy3-dUTP was used. The amplification and labelling of mRNA were performed using Low RNA Linear Amplification Kit (Agilent technologies), following manufacturer’s protocol
|
| Label |
Cy3
|
| Label protocol |
1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.
|
| Scan protocol |
After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer´s protocol.
|
| Data processing |
The slides were analyzed using Feature Extraction Software 10.0 (Agilent technologies), following manufacturer’s protocol. A hierarchical clustering method was applied to group the genes and samples on the basis of the similarities in expression and the unsupervised analyses were visualized using the SOTA and TreeView software assuming euclidean distances between genes (http://bioinfo.cnio.es/cgi-bin/tools/clustering/sotarray). Genes with potentially significant changes in expression were identified using the POMELO program (http://www.genoma.wi.mit.edu/MPR/software). We tested the null hypothesis of equal means among groups using T-test, computing p-values using a permutation test. To select differentially expressed genes, we adjusted for multiple testing using the False Discovery Rate (FDR) method (Chung et al, 2004)
|
| |
|
| Submission date |
May 27, 2011 |
| Last update date |
Oct 22, 2011 |
| Contact name |
Gema Moreno-Bueno |
| E-mail(s) |
gmoreno@iib.uam.es
|
| Phone |
+34914978974
|
| Organization name |
IIB
|
| Department |
Biochemistry
|
| Lab |
1.13
|
| Street address |
Arturo Duperier
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL887 |
| Series (1) |
| GSE29581 |
Lysyl oxidase-like 2 (LOXL2) a new regulator of cell polarity required for metastatic dissemination of basal-like breast carcinomas |
|
