|
| Status |
Public on May 12, 2010 |
| Title |
P2M-3 |
| Sample type |
RNA |
| |
|
| Source name |
Passage 2 cells mesenchymal
|
| Organism |
Mus musculus |
| Characteristics |
strain: Pten Loxp/loxp;Alb-Cre
genome/variation: Liver-specific Pten deletion
tissue: liver
cell type: liver tumor cells
cell morphology: mesenchymal
cell passage: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
Replicate 3
|
| Data processing |
Raw data was extracted from Illumina's Beadstudio v3.0. Normalization was done in Beadstudio v.3 using the Average Normalization method. The data were then converted to t16 log2 ratios. This was done to generate sufficient number of data points for a one sample t-test (4 replicates for each sample; 4x4). One sample t-test was performed using Tigr MEV v4.4 with p<0.05. Probe sets with at least a 1.4 fold were considered for the final candidate gene list.
|
| |
|
| Submission date |
Sep 24, 2009 |
| Last update date |
May 12, 2010 |
| Contact name |
Wei Ding |
| Organization name |
Pennsylvania State University College of Medicine
|
| Department |
Pediatrics
|
| Lab |
Rountree Lab
|
| Street address |
500 University Drive
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE18255 |
Epithelial-to-Mesenchymal Transition of Murine PTEN-/- Liver Tumor Cells Promotes Tumor Growth and Invasion |
|
