|
| Status |
Public on Apr 02, 2015 |
| Title |
PBM_P_Nb38 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood monocytes, non-metastatic patient
|
| Organism |
Homo sapiens |
| Characteristics |
tumor stage: non-metastatic patient
gender: F
age: 54
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser, and quantification with Nanodrop.
|
| Label |
Cy3
|
| Label protocol |
Biotynilated cRNA was prepared with Ambion Illumina TotalPrep RNA Amplification Kit
|
| |
|
| Hybridization protocol |
Illumina Whole-Genome Gene Expression Direct Hybridization Assay
|
| Scan protocol |
Standard Illumina Scanning protocol
|
| Description |
5937302002_G
|
| Data processing |
With GenomeStudio GX (version 1.5.4) we extracted from each array the background-corrected, summarized expression levels (AVG Signal), standard errors of the bead replicates (BEAD STERR), number of beads used (Avg NBEADS) and detection scores (Detection Pval). Subsequently, we applied a variance stabilizing transformation and a quantile normalization in R, as implemented in the lumi-package from Bioconductor.
|
| |
|
| Submission date |
Jun 07, 2013 |
| Last update date |
Apr 02, 2015 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE47756 |
Tumor-educated circulating monocytes are powerful specific biomarkers for diagnosis of colorectal cancer |
|
