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Sample GSM1563501 Query DataSets for GSM1563501
Status Public on May 21, 2015
Title 33D3_Untreated_786-O
Sample type RNA
 
Source name Frozen 786-O Xenograft Tumors
Organism Homo sapiens
Characteristics treatment: Frozen 786-O Untreated Sorafenib
host organism: Mus musculus
cell type: renal cell carcinoma
cell line: 786-O
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 786-O Untreated
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
ID_REF
VALUE MAS 5.0 Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 585.766 P 0.000753643
AFFX-BioB-M_at 798.443 P 5.16732e-05
AFFX-BioB-3_at 453.247 P 0.000581214
AFFX-BioC-5_at 1530.16 P 5.16732e-05
AFFX-BioC-3_at 1954.05 P 4.42873e-05
AFFX-BioDn-5_at 5439.06 P 4.42873e-05
AFFX-BioDn-3_at 9671.5 P 8.14279e-05
AFFX-CreX-5_at 21415.7 P 5.16732e-05
AFFX-CreX-3_at 26840 P 4.42873e-05
AFFX-DapX-5_at 14861.3 P 4.42873e-05
AFFX-DapX-M_at 19698.3 P 5.16732e-05
AFFX-DapX-3_at 19343.8 P 4.42873e-05
AFFX-LysX-5_at 2040.75 P 5.16732e-05
AFFX-LysX-M_at 2263.43 P 4.42873e-05
AFFX-LysX-3_at 4679.36 P 4.42873e-05
AFFX-PheX-5_at 3637.2 P 4.42873e-05
AFFX-PheX-M_at 4581.6 P 4.42873e-05
AFFX-PheX-3_at 3195.62 P 4.42873e-05
AFFX-ThrX-5_at 4307.72 P 6.02111e-05
AFFX-ThrX-M_at 5962.58 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1631 Kbytes.




Supplementary file Size Download File type/resource
GSM1563501_33D3.CEL.gz 5.2 Mb (ftp)(http) CEL
GSM1563501_33D3.mas5.CHP.gz 485.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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