|
| Status |
Public on May 22, 2014 |
| Title |
empty vector 72h rep2 |
| Sample type |
RNA |
| |
|
| Source name |
BE(2)-C cell line
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: pTRex-Dest30
time (h): 72
cell line: BE(2)-C
|
| Treatment protocol |
transfection with 2µg plasmid using effectene (Qiagen)
|
| Growth protocol |
DMEM 10% fetal bovine serum; 1% non-essential amino acids
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cell lines with the RNeasy Mini Kit (Qiagen) acording to manufacture protocol.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA samples for hybridization on Illumina Human Sentrix-12 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol
|
| |
|
| Hybridization protocol |
Illumina standard hybridization protocol
|
| Scan protocol |
Microarray scanning was done using an iScan array scanner and Illumina standard protocol.
|
| Data processing |
Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.
The data were normalized using quantile normalization in R
|
| |
|
| Submission date |
May 28, 2013 |
| Last update date |
May 22, 2014 |
| Contact name |
Johannes Fabian |
| URL |
http://www.dkfz.de/en/PaedOnko/index.php
|
| Organization name |
German Cancer Research Center
|
| Department |
CCU Pediatric Oncology
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE47407 |
GRHL1 acts as a tumor suppressor in neuroblastoma and is negatively regulated by MYCN and HDAC3 |
|
