|
| Status |
Public on Jun 28, 2012 |
| Title |
CxSCC32 |
| Sample type |
RNA |
| |
|
| Source name |
cervical squamous cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
hpv: high-risk HPV positive
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10 micrometer frozen sections of all tissue samples were first subjected to laser capture microdissection using a Leica ASLMD microscope (Leica, Heidelberg, Germany) to enrich for neoplastic, dysplastic or normal epithelial cells as described previously (Wilting et al, Genes, Chromosomes Cancer 2008). Total RNA was isolated from microdissected tissue samples using TRIzol Reagent according to the manufacturers’ instructions. To ensure comparable RNA integrity between specimens analysed by array, RNA pico chips were performed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).
|
| Label |
Cy3
|
| Label protocol |
Labelling was performed according to the manufacturers’ instructions. In short, miRNAs were dephoshorylated using Calfs Intestine Phosphatase (CIP) and a Cy3 labelled dCTP was ligated to the miRNA.
|
| |
|
| Hybridization protocol |
Hybridisation buffer as supplied by the manufacturer was added to the mixture and this was hybridised for 20 hours at 55 degrees at a rotation speed of 20 rpm.
|
| Scan protocol |
scanning was performed using a G2505B scanner (Agilent) using the protocol designed for the used platform by the manufacturer (Agilent).
|
| Description |
VUMC_CxSCC32_12325
|
| Data processing |
The obtained single-channel microarray data were log-transformed and normalised using quantile normalisation. Probes with intensities below 64 in more than 90% of the samples were discarded as it was assumed that hybridisation for this probe was inefficient (n=44). For the 428 remaining probes (representing 213 miRNAs) the intensity values were averaged per probe for further analyses.
|
| |
|
| Submission date |
Jul 14, 2011 |
| Last update date |
Jun 30, 2012 |
| Contact name |
Daoud Sie |
| E-mail(s) |
d.sie@vumc.nl
|
| Phone |
+31 20 4442428
|
| Organization name |
Vrije Universiteit Medical Center
|
| Department |
Pathology
|
| Lab |
Microarray Core Facility
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6955 |
| Series (1) |
| GSE30656 |
Altered microRNA expression associated with chromosomal and epigenetic changes contributes to cervical carcinogenesis |
|
