|
| Status |
Public on Feb 28, 2012 |
| Title |
1_3dox- |
| Sample type |
RNA |
| |
|
| Source name |
NT2D1 cell line, total RNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: embryonal carcinoma cell line
cell line: NT2D1
genotype/variation: stably expressing TetR3 and L1TD1shRNA
dox treatment: dox-
time point: Day 6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Kit (Qiagen). To eliminate genomic DNA DNase I (Qiagen) digestion in column was included. RNA/cRNA concentrations where checked with Nanodrop ND-1000 and RNA/cRNA quality was controlled by BioRad’s Experion electrophoresis station
|
| Label |
biotin
|
| Label protocol |
Ambion's Illumina RNA TotalPrep Amplification kit (cat no AMIL1791)
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
replicate 2
|
| Data processing |
The data was analyzed with R language and environment for statistical computing (version 2.10.1) using the Bioconductor module (version 2.5), quantile normalization method from limma package was used. Limma package computed normalized signal intensities.
|
| |
|
| Submission date |
Apr 09, 2010 |
| Last update date |
Feb 28, 2012 |
| Contact name |
Nelly Rahkonen |
| E-mail(s) |
nelly.rahkonen@btk.fi
|
| Organization name |
Turku Centr for Biotechnology
|
| Street address |
Tykistökatu 6 A
|
| City |
Turku |
| ZIP/Postal code |
20520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL6947 |
| Series (1) |
| GSE21275 |
Genome wide analysis of long term L1TD1 knockdown effects in NT2D1 cell line with inducible shRNA vectors |
|
