|
| Status |
Public on Jul 20, 2021 |
| Title |
CSU-004 tumor pre-treatment replicate A |
| Sample type |
RNA |
| |
|
| Source name |
Osteosarcoma
|
| Organism |
Canis lupus familiaris |
| Characteristics |
breed: Mix breed
Sex: Male
neutered status: Yes
age (years): 5.16
time to progression (days): 90
overall survival (days): 228
body weight (kgs): 70
alkaline phosphatase levels: 38
monocyte counts (1000 cells/μl): 0.4
number of doxorubicin treatments: 3
number of carboplatin treatments: 0
|
| Treatment protocol |
Tumor samples were frozen in liquid N2, pulverized to a powder by freeze-fracture using a manual Bio-Pulverizer
|
| Growth protocol |
Following diagnosis and amputation of the affected limb, biopsy material was collected using a Michele Trephine bone biopsy instrument and collected biopsies reviewed by a veterinary pathologist for assessment of the percent of viable tumor present within each sample. Two samples from each tumor with the highest percent viable tumor were selected for mRNA isolation and subsequent Affymetrix Canine 2.0 microarray analysis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions, total RNA was further purified using Qiagen RNeasy Purification Kits.
|
| Label |
biotin
|
| Label protocol |
Reverse transcription of cRNA as well as cRNA in vitro transcription, amplification, purification, biotin-labeling, and fragmentation were performed using a GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix, Cat. 902416) following manufacturer instructions.
|
| |
|
| Hybridization protocol |
Fragmented and labeled cRNA were frozen at -20°C and overnight shipped on dry ice to the University of Colorado Cancer Center Genomics and Miroarray Shared Resource (University of Colorado, Anschutz Medical Campus, Aurora, CO) where Hybridized chips were washed, stained and scanned using an Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
The Affymetrix GeneChip scanner 3000 7G was used to acquire images
|
| Description |
Gene expression data from osteosarcoma sample CSU-004A
|
| Data processing |
The data were analyzed in R using RMA and COMBAT normalization methods for batch correction.
|
| |
|
| Submission date |
Jul 17, 2021 |
| Last update date |
Jul 20, 2021 |
| Contact name |
Sunetra Das |
| E-mail(s) |
sdas@colostate.edu
|
| Organization name |
Colorado State University
|
| Department |
Clinical Sciences
|
| Street address |
300 W Drake Rd
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80526 |
| Country |
USA |
| |
|
| Platform ID |
GPL3738 |
| Series (1) |
| GSE180303 |
Predictive Models of Drug Response in Canine Osteosarcoma: A Prospective Clinical Trial Testing the COXEN Approach |
|
