|
| Status |
Public on Nov 30, 2022 |
| Title |
111_tumor |
| Sample type |
RNA |
| |
|
| Source name |
Oral Cavity
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
g: G3
t: T4
n: N+
hpv: HPV-
tissue: Oral Cavity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the RNeasy kit (Qiagen) following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
For miRNA microarray, 100 ng of RNA was labeled (Cy3) and hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.
|
| |
|
| Hybridization protocol |
For miRNA microarray, 100 ng of RNA was labeled (Cy3) and hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.
|
| Scan protocol |
Scanning and image analysis were performed using the Agilent DNA Microarray Scanner (P/N G2565BA) equipped with extended dynamic range (XDR) software, according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Protocol manual. Feature Extraction Software (Version 10.5) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol
|
| Data processing |
signal intensities were extracted by Agilent Feature Extraction 10.7.3.1 software. The arrays were normalized by dividing by the mean intensity only using the 25th and 75th percentile range of the data. Intensity level of each miRNA was scaled by the median of the distribution of the miRNA for samples processed in the first chip version and by the median of the distribution of the miRNA for samples processed in the second chip version, and all values multiplied for the mean value between the two medians. Data were log2-trasformed. For the analyses we consider just miRNAs common at the two platforms and miRs that were absent across all samples were removed. miRNAs not expressed were excluded
|
| |
|
| Submission date |
Oct 26, 2022 |
| Last update date |
Dec 01, 2022 |
| Contact name |
andrea sacconi |
| Organization name |
regina elena cancer institute
|
| Street address |
via elio chianesi
|
| City |
rome |
| ZIP/Postal code |
00144 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16770 |
| Series (1) |
| GSE216630 |
Samples from prospectively enrolled patients with histologically confirmed primary Head and Neck squamous cell carcinoma (HNSCC) were analyzed for miRNA profiling |
|
