|
| Status |
Public on Mar 01, 2017 |
| Title |
PDX + control (rep2) |
| Sample type |
RNA |
| |
|
| Source name |
PDX_control_597
|
| Organism |
Homo sapiens |
| Characteristics |
pdx: HCC patient derived xenografts
treatment: regular food
|
| Treatment protocol |
Before harvesting, HepG2 cells were incubated 6h with 10μM of NEN, 10μM of niclosamide, DMSO control. Treatment was initiated within one week after transplantation of the Patient Derived Xenograft (PDX). For each PDX model, tumor-bearing mice with similar initial bioluminescence signals were allocated into three groups (n=5 each), to be given daily: 1) NEN (200 mg/kg) mixed in autoclaved food, or 2) regular food, for six weeks. Tumor cells were harvested for the microarray experiment.
|
| Growth protocol |
HepG2 cells were seeded at 20% confluency, and grown 72h in Eagle’s MEM containing 10% FBS, penicillin and streptomycin at 37ºC and 5% CO2. To build PDX models, HCC tissues were collected from HCC patients who had undergone liver resection as part of their treatment. Single tumor cells labeled with luciferase gene were suspended in BEME medium containing 50% Matrix Matrigel, and then subcutaneously injected into 4–8 week old male NSG mice (20-25 g body weight). Tumor development was monitored daily. Once the subcutaneous xenograft reached 1 cm in diameter, it was removed and cut into 2 mm pieces and surgically implanted into the left lobe of the liver of another group of 6 weeks old NSG mice. Tumor growth was monitored once a week using the Xenogen IVIS in vivo imaging system (Caliper Life Sciences, Hopkinton, CA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)
|
| |
|
| Hybridization protocol |
Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer
|
| Scan protocol |
Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner
|
| Description |
replicate 2
|
| Data processing |
Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). Array probes transformed by logarithm and normalized by quantile method.
|
| |
|
| Submission date |
Jan 27, 2016 |
| Last update date |
Mar 01, 2017 |
| Contact name |
Bin Chen |
| E-mail(s) |
chenbi12@msu.edu
|
| Organization name |
Michigan State University
|
| Street address |
15 Michigan St. NE
|
| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE77322 |
Niclosamide ethanolamine reverses gene expression and inhibits growth of hepatocellular carcinoma in vitro and in vivo |
|
