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Sample GSM1131228 Query DataSets for GSM1131228
Status Public on Jul 01, 2013
Title U2OS No Treatment, Replicate 3
Sample type RNA
 
Source name U2OS No Treatment
Organism Homo sapiens
Characteristics cell line: U2OS
cell type: osteosarcoma
agent: No Treatment (control for Doxorubicin-treated cells)
Treatment protocol for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
Growth protocol U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
Label biotin
Label protocol One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
 
Hybridization protocol 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
Scan protocol Arrays were scanned in an Affymetrix Scanner 3000.
Description U2OS No Treatment control 24 hr, control for Doxorubicin-treated cells
Data processing data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
 
Submission date Apr 30, 2013
Last update date Jul 01, 2013
Contact name NIEHS Microarray Core
E-mail(s) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL570
Series (2)
GSE46493 Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells (Affymetrix)
GSE46642 Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells

Data table header descriptions
ID_REF
VALUE MAS 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 879.585 P 0.000146581
AFFX-BioB-M_at 1174.4 P 4.42873e-05
AFFX-BioB-3_at 787.197 P 4.42873e-05
AFFX-BioC-5_at 2085.52 P 5.16732e-05
AFFX-BioC-3_at 2805.08 P 5.16732e-05
AFFX-BioDn-5_at 5537.87 P 4.42873e-05
AFFX-BioDn-3_at 12845.1 P 7.00668e-05
AFFX-CreX-5_at 27775.8 P 5.16732e-05
AFFX-CreX-3_at 30557.5 P 4.42873e-05
AFFX-DapX-5_at 1101.31 P 4.42873e-05
AFFX-DapX-M_at 2272.13 P 0.000224668
AFFX-DapX-3_at 3109.24 P 4.42873e-05
AFFX-LysX-5_at 159.315 P 0.000509415
AFFX-LysX-M_at 165.974 P 0.00556451
AFFX-LysX-3_at 355.655 P 0.000126798
AFFX-PheX-5_at 195.424 P 4.42873e-05
AFFX-PheX-M_at 331.783 P 0.000195116
AFFX-PheX-3_at 254.779 P 0.000389797
AFFX-ThrX-5_at 204.87 P 7.00668e-05
AFFX-ThrX-M_at 332.854 P 0.000258358

Total number of rows: 54675

Table truncated, full table size 1643 Kbytes.




Supplementary file Size Download File type/resource
GSM1131228_11450_U2OS_No_Treatment_Rep_3_HG-U133_Plus_2_.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM1131228_11450_U2OS_No_Treatment_Rep_3_HG-U133_Plus_2_.mas5.CHP.gz 486.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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