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Sample GSM1563508 Query DataSets for GSM1563508
Status Public on May 21, 2015
Title 35B7_Resistant_A498
Sample type RNA
Source name Frozen A498 Xenograft Tumors
Organism Homo sapiens
Characteristics treatment: Frozen A498 Resistant Sorafenib
host organism: Mus musculus
cell type: renal cell carcinoma
cell line: A498
Treatment protocol biopsy specimens were snap frozen at time of mouse surgery, then stored at -80C until time of total RNA extraction
Growth protocol Female athymic nude/beige mice (Charles River Laboratories, MA) were used for subcutaneous xenograft tumor models. All experiments were approved by the Beth Israel Deaconess Medical Center Institutional Animal Care and Use Committee. To establish RCC tumor xenografts, 1 x 10^7 786-O or A498 tumor cells were prepared and injected subcutaneously into the flanks of 6-8 week old mice. To ensure a consistent size at the outset of treatment, tumors were measured with calipers daily once they reached a diameter of 3-5 mm. Sunitinib (additive-free, 53.6 mg/kg) was administered 6 out of 7 days per week by gavage beginning when the tumors had grown to a diameter of 12 mm. Sorafenib (80 mg/kg, Bayer) was administered 6 out of 7 days per week by gavage beginning when the tumors had grown to a diameter of 12 mm. Treated and control tumors were again measured daily during therapy.
Extracted molecule total RNA
Extraction protocol Trizol extraction was performed after tumor were excised and frozen
Label biotin
Label protocol Standard Affymetrix Protocol
Hybridization protocol The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.
Scan protocol The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).
Description Frozen A498 Resistant Sorafenib
Data processing The data was normalised using Robust Multichip Average (RMA), Dchip and MAS5 algorithms
Submission date Dec 10, 2014
Last update date May 21, 2015
Contact name Manoj Bhasin
Phone 6176670009
Organization name Beth Israel Deaconess Medical Center
Street address 330 Brookline Avenue RN 380E
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL570
Series (1)
GSE64052 Gene expression changes during resistance toward vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitor (TKI) therapy in renal cell carcinoma (RCC)

Data table header descriptions
VALUE MAS 5.0 Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 572.305 P 0.000753643
AFFX-BioB-M_at 749.541 P 4.42873e-05
AFFX-BioB-3_at 589.858 P 7.00668e-05
AFFX-BioC-5_at 1922.08 P 5.16732e-05
AFFX-BioC-3_at 2772.58 P 4.42873e-05
AFFX-BioDn-5_at 4404.65 P 4.42873e-05
AFFX-BioDn-3_at 7066.66 P 7.00668e-05
AFFX-CreX-5_at 19678.4 P 5.16732e-05
AFFX-CreX-3_at 22740.7 P 4.42873e-05
AFFX-DapX-5_at 5468.91 P 4.42873e-05
AFFX-DapX-M_at 8380.98 P 5.16732e-05
AFFX-DapX-3_at 9640.63 P 4.42873e-05
AFFX-LysX-5_at 734.308 P 4.42873e-05
AFFX-LysX-M_at 823.451 P 5.16732e-05
AFFX-LysX-3_at 1443.74 P 5.16732e-05
AFFX-PheX-5_at 1168.18 P 4.42873e-05
AFFX-PheX-M_at 1456.95 P 4.42873e-05
AFFX-PheX-3_at 925.866 P 4.42873e-05
AFFX-ThrX-5_at 1556.11 P 5.16732e-05
AFFX-ThrX-M_at 2132.68 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1646 Kbytes.

Supplementary file Size Download File type/resource
GSM1563508_35B7.CEL.gz 5.2 Mb (ftp)(http) CEL
GSM1563508_35B7.mas5.CHP.gz 481.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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