|
| Status |
Public on Dec 23, 2014 |
| Title |
13282 |
| Sample type |
RNA |
| |
|
| Source name |
25W DEN + 5W IgG surrounding tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129S2/SvPasCrl
gender: male
age: 210 days
tissue: liver (non-tumor)
induction: 25W diethylnitrosamine
treatment: 5 weeks IgG-control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen
|
| Label |
Cy3
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| Hybridization protocol |
Purified and labeled cRNA (600 ng of Cy3 labeled cRNA) was hybridised on Agilent Sureprint G3 Mouse GE 8x60k Microarrays followed by (manual) washing, according to the manufacturer’s procedures.
|
| Scan protocol |
To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).
|
| Description |
25W DEN + 5W IgG (control) surrounding (non-tumour) tissue
|
| Data processing |
The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v10.7.3.1) after an additional quantile normalization. Intensities were base 2 log-transformed.
|
| |
|
| Submission date |
Jan 24, 2012 |
| Last update date |
Dec 23, 2014 |
| 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 |
GPL10787 |
| Series (1) |
| GSE35289 |
Placental growth factor as potential target against hepatocellular carcinoma in an orthotopic mouse model. |
|
