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Sample GSM5460474 Query DataSets for GSM5460474
Status Public on Jul 20, 2021
Title CSU-007 tumor pre-treatment replicate C
Sample type RNA
 
Source name Osteosarcoma
Organism Canis lupus familiaris
Characteristics breed: Malamute
Sex: Male
neutered status: Yes
age (years): 4.93
time to progression (days): 77
overall survival (days): 119
body weight (kgs): 56
alkaline phosphatase levels: 54
monocyte counts (1000 cells/μl): 0.5
number of doxorubicin treatments: 0
number of carboplatin treatments: 3
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-007C
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

Data table header descriptions
ID_REF
VALUE RMA-COMBAT normalized signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 8.936864706
AFFX-BioB-5_at 9.011937334
AFFX-BioB-M_at 9.279297688
AFFX-BioC-3_at 10.7760225
AFFX-BioC-5_at 10.39695711
AFFX-BioDn-3_at 12.5843313
AFFX-BioDn-5_at 11.70435151
AFFX-Cf_Actin_3_at 12.99292963
AFFX-Cf_Actin_5_s_at 12.38867422
AFFX-Cf_Actin_M_at 11.81556492
AFFX-Cf_AdrenRecpt_3_at 6.926799279
AFFX-Cf_AdrenRecpt_5_at 4.850314135
AFFX-Cf_AdrenRecpt_M_at 4.934367008
AFFX-Cf_G-6-PDH_3_at 3.547946146
AFFX-Cf_G-6-PDH_5_at 4.130458889
AFFX-Cf_G-6-PDH_M_at 3.683549682
AFFX-Cf_Gapdh_3_at 13.49276314
AFFX-Cf_Gapdh_5_at 12.93501433
AFFX-Cf_Gapdh_M_at 12.93786099
AFFX-Cf_P450-2E1_3_s_at 2.91678393

Total number of rows: 43035

Table truncated, full table size 1271 Kbytes.




Supplementary file Size Download File type/resource
GSM5460474_T7C.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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