|
| Status |
Public on Dec 23, 2015 |
| Title |
tumor tissue patient p3 |
| Sample type |
RNA |
| |
|
| Source name |
prostate cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: tumor
patient: p3
batch: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA with miRNA fraction was extracted from cell lines with miRNeasy mini kit (Qiagen) according to manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol for Illumina BeadArray reader
|
| Description |
4493851045_C
|
| Data processing |
Raw data were obtained from scanned images using Illumina BeadStudio v3.3.8 and pre-processed in R using the Bioconductor package lumi. Raw expression data were log2-transformed and normalized using the robust spline normalization method. After quality control a batch effect was observed and removed using the ComBat method implemented in the Bioconductor package sva.
|
| |
|
| Submission date |
Dec 22, 2015 |
| Last update date |
Dec 23, 2015 |
| Contact name |
Matteo Dugo |
| E-mail(s) |
dugo.matteo@hsr.it
|
| Organization name |
IRCCS Ospedale San Raffaele
|
| Department |
Department of Medical Oncology
|
| Street address |
via Olgettina 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL8179 |
| Series (1) |
| GSE76260 |
miRNA expression profiling in prostate cancer and non-neoplastic tissues |
|
