|
| Status |
Public on May 13, 2016 |
| Title |
Control3 |
| Sample type |
RNA |
| |
|
| Source name |
removed tumor, vehicle alone
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: pancreatic cancer cell line BxPC-3
treatment: Control
tissue: removed tumor
|
| Treatment protocol |
Pancreatic cancer cells (BxPC-3) in culture were harvested and viable cells (5 × 106 cells) were injected subcutaneously into the backs of the mice. When tumor volumes reached 150 mm3, treatment began. The treatment group of mice received Deferasirox suspended in saline, which was administered by oral gavage every second day, with three treatments per week, over 21 days at concentrations of 200 mg/kg. The control mice were treated with the vehicle alone. At the end of the experiment, the mice were sacrificed and the tumors were excised and processed for genetic analyses.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
|
| Description |
Gene expression after administration of Vehicle alone
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.
|
| |
|
| Submission date |
May 12, 2016 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Hirofumi Harima |
| E-mail(s) |
harima@yamaguchi-u.ac.jp
|
| Organization name |
Yamaguchi University Graduate School of Medicine
|
| Department |
Department of Gastroenterology and Hepatology
|
| Street address |
Minami Kogushi 1-1-1
|
| City |
Ube |
| State/province |
Yamaguchi |
| ZIP/Postal code |
755-8505 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE81363 |
Investigation of gene expression alterations of pancreatic cancer caused by Deferasirox administration |
|
| Relations |
| Reanalyzed by |
GSE113533 |
