|
| Status |
Public on Apr 07, 2018 |
| Title |
PDXEx-C |
| Sample type |
RNA |
| |
|
| Source name |
ex-vivo tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: IBC patient-derived xenograft (PDX)-derived ex vivo tumor tissue
original tumor type: triple negative inflammatory breast cancer
|
| Treatment protocol |
To compare the molecular signatures, we utilized magnetic 3D bio-printing (n3D BiosciencesTM, Inc.). Briefly, viable cells released from the PDX tumor and tagged with poly-L-lysine–tagged magnetic nanoparticle assembly for 24hr were harvested and dispensed into a 96-well ultra-low attachment tissue culture plate at a concentration of 50,000 cells per well, and the plate was placed on a 96 well magnetic bioprinter. Well-formed and equally sized PDXEx “bio-prints” were observed at 5 days of incubation, a time corresponding to the duration of the planned high-throughput drug screens.
|
| Growth protocol |
Cells harvested from IBC PDX tumors were incubated overnight with poly-L-lysine–covered iron nanoparticles for about 18-24 h at a ratio of 1 µL of nanoshells to 150,000 cells to permit the binding of the iron nanoparticles to the surface of the cells. The nanoparticle-coated cells were then placed in the Bio-Assembler system. Cells were maintained within the Bio-Assembler system for 10 to 14 days at 370C in a humidified environment with medium changed every 3 to 4 days. The best results were obtained from cells released from PDX tumors that were vascular with a fat content between 20% and 30% of the total tumor weight. Tumors weighing 0.8 gram to 1 gram generally yielded the best results.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated from the PDX tumors as well as from the ex vivo tumor tissue after 5 days of growth in culture was purified with the Trizol method (Invitrogen) according to the manufacturer’s instructions
|
| Label |
biotin
|
| Label protocol |
The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom D array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.
|
| Scan protocol |
GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.
|
| Description |
07_Tumor C star_(Clariom_D_Human).CEL(normalized)
|
| Data processing |
Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.
|
| |
|
| Submission date |
Nov 08, 2017 |
| Last update date |
Apr 07, 2018 |
| Contact name |
Geoffrey Arthur Bartholomeusz |
| E-mail(s) |
[email protected]
|
| Phone |
713-792-4158
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Experimental Therapeutics
|
| Street address |
1901 East Road
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE106685 |
Ex-vivo screening platform to identify tumor-specific therapies |
|
