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Sample GSM1131229 Query DataSets for GSM1131229
Status Public on Jul 01, 2013
Title U2OS Doxorubicin treated, Replicate 1
Sample type RNA
 
Source name U2OS Doxorubicin treated
Organism Homo sapiens
Characteristics cell line: U2OS
cell type: osteosarcoma
agent: Doxorubicin
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 cells treated with 0.6 ug/ml Doxorubicin for 24 hr
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 824.163 P 0.000195116
AFFX-BioB-M_at 1370.51 P 4.42873e-05
AFFX-BioB-3_at 846.59 P 4.42873e-05
AFFX-BioC-5_at 2123.44 P 5.16732e-05
AFFX-BioC-3_at 2899.21 P 4.42873e-05
AFFX-BioDn-5_at 5541.36 P 4.42873e-05
AFFX-BioDn-3_at 11836 P 6.02111e-05
AFFX-CreX-5_at 29547.5 P 5.16732e-05
AFFX-CreX-3_at 30287.4 P 4.42873e-05
AFFX-DapX-5_at 1736.32 P 4.42873e-05
AFFX-DapX-M_at 3951.72 P 0.000146581
AFFX-DapX-3_at 6016.49 P 4.42873e-05
AFFX-LysX-5_at 266.546 P 0.00010954
AFFX-LysX-M_at 340.847 P 0.00141043
AFFX-LysX-3_at 761.028 P 7.00668e-05
AFFX-PheX-5_at 465.762 P 5.16732e-05
AFFX-PheX-M_at 564.53 P 0.000126798
AFFX-PheX-3_at 467.409 P 7.00668e-05
AFFX-ThrX-5_at 289.378 P 0.000856509
AFFX-ThrX-M_at 526.696 P 0.000169227

Total number of rows: 54675

Table truncated, full table size 1641 Kbytes.




Supplementary file Size Download File type/resource
GSM1131229_11454_U2OS_Doxo_Rep_1_HG-U133_Plus_2_.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM1131229_11454_U2OS_Doxo_Rep_1_HG-U133_Plus_2_.mas5.CHP.gz 487.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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