|
| Status |
Public on Nov 01, 2013 |
| Title |
tumoral tissue specimen BB51 |
| Sample type |
RNA |
| |
|
| Source name |
oral cavity
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
tnm grading: T2
lymphonode metastasis: N+
tumor stage: III
age: 61
grade of differentiation: 2
|
| Treatment protocol |
All healthy and 119 neoplastic specimens, sampled as fresh tissue, were processed for molecular analyses according to the following scheme: each biopsy was dissected in three 1.5 cm-thick cubes, immersed into RNAlater Solution (Ambion) and frozen at -80°C. One of the three samples was used to extract total RNA for qPCR analyses, whereas the other two samples were used to create a tissue bank.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each biopsy was extracted using Trizol® according to the manufacturer’s instructions and in combination with Qiagen RNAeasy Mini Kit (Qiagen). RNA integrity and was verified using Thermo Scientific NanoDropTM spectrophotometers and micro-electrophoresis on a Bioanalyzer 2010 instrument (Agilent). Total RNA (1μg) was reverse-transcribed with the QuantiTect® Reverse Transcription Kit (Qiagen) according to the manufacturer’s instructions and cDNA was quantified
|
| Label |
TaqMan assay labels were preloaded on the CARDs
|
| Label protocol |
An equal amount of input cDNA (200 ng) was used per reaction and loaded in one of the eight sample-loading port on TaqMan Low Density Array (Applied Biosystems) and cards were run on ABI PRISM 7900 HT Fast Real-Time PCR System (Applied Biosystems Inc., Foster City, CA, USA). For data analysis we used the RQ Manager and Data Assist softwares provided by Applied Biosystem Inc.
|
| |
|
| Hybridization protocol |
n/a
|
| Scan protocol |
n/a
|
| Description |
tumoral tissue specimen
|
| Data processing |
The normalization and all the data analysis were performed according to the manufacturers instructions using Data Assist software (Applied Biosystems); it were excluded all Ct raw data ≥35 Ct and were exclude outliers among replicates; p-values were adjusted using Benjamini-Hochberg False Discovery Rate.
For the normalization it used the average of all replicates of the 18S housekeeping gene (18S-Hs99999901_s1 assay) and software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data; matrix normalized worksheet reports normalized signal (against housekeeping gene); Fold Change worksheet reports ratios between patients samples and reference sample (HEALTHY).
|
| |
|
| Submission date |
Nov 17, 2011 |
| Last update date |
Nov 01, 2013 |
| Contact name |
Silvia Rossi |
| E-mail(s) |
silvia.rossi1@unipr.it
|
| Phone |
+390521905655
|
| Organization name |
COMT - Centre for Molecular and Translational Oncology, University of Parma
|
| Department |
Genetics, Microbiology, Anthropology ed Evolution
|
| Lab |
Prof. Perris
|
| Street address |
Viale Usberti, 11/A
|
| City |
Parma |
| State/province |
Parma |
| ZIP/Postal code |
43124 |
| Country |
Italy |
| |
|
| Platform ID |
GPL14900 |
| Series (1) |
| GSE33788 |
Surface proteoglycans expressions in oral squamous cell carcinoma |
|
