|
| Status |
Public on Dec 29, 2011 |
| Title |
p53_ko_9849T3 |
| Sample type |
RNA |
| |
|
| Source name |
Trp53 ko liver tumor (HCC/CCC; not treated)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: hepatocellular carcinoma (HCC)/cholangiocellular carcinoma (CCC)
background strain: C57BL/6J
genotype: Trp53 ko
treatment: none
|
| Treatment protocol |
Mice (group: DEN-induced liver tumors) were treated at day 15 with DEN (i.p.; 10µg/g bodyweight).
|
| Growth protocol |
Mice were kept in a pathogen-free environment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer.
|
| |
|
| Hybridization protocol |
1.65 µg of Cy3-labeled cRNA (specific activity >8.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 55 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K V2 Microarrays (G4846A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the Agilent Scan Control Version A.8.4.1.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). The data was preprocessed according to Agilent's GeneSpring software standard workflow. Gene expression levels were background corrected and signals for duplicated probes were summarized by geometric mean of non-compromised probes. After log2 transformation, a percentile shift normalization at the 75% level and a baseline shift to the median baseline of all probes was performed.
|
| |
|
| Submission date |
Dec 28, 2011 |
| Last update date |
Jan 09, 2012 |
| Contact name |
Hans A Kestler |
| E-mail(s) |
[email protected]
|
| Phone |
+49 731 5024248
|
| Organization name |
University of Ulm
|
| Department |
Research Group Bioinformatics and Systems Biology
|
| Street address |
Albert-Einstein-Allee 11
|
| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE34760 |
p53 deletion induces liver carcinoma with bilineal differentiation |
|
