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Sample GSM1131232 Query DataSets for GSM1131232
Status Public on Jul 01, 2013
Title U2OS DMSO treated, Replicate 1
Sample type RNA
Source name U2OS DMSO treated
Organism Homo sapiens
Characteristics cell line: U2OS
cell type: osteosarcoma
agent: DMSO (control for Nutlin-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 cells treated with 0.1% DMSO for 24 hr, control for Nutlin-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
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
VALUE MAS signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 924.343 P 5.16732e-05
AFFX-BioB-M_at 1338.81 P 4.42873e-05
AFFX-BioB-3_at 804.151 P 4.42873e-05
AFFX-BioC-5_at 2698.56 P 5.16732e-05
AFFX-BioC-3_at 3863.69 P 4.42873e-05
AFFX-BioDn-5_at 6894.01 P 4.42873e-05
AFFX-BioDn-3_at 11622.5 P 4.42873e-05
AFFX-CreX-5_at 32613.5 P 5.16732e-05
AFFX-CreX-3_at 30387.9 P 4.42873e-05
AFFX-DapX-5_at 1286.81 P 4.42873e-05
AFFX-DapX-M_at 2566.92 P 0.000224668
AFFX-DapX-3_at 3410.36 P 4.42873e-05
AFFX-LysX-5_at 169.538 P 8.14279e-05
AFFX-LysX-M_at 228.65 P 0.00227496
AFFX-LysX-3_at 406.832 P 5.16732e-05
AFFX-PheX-5_at 268.675 P 6.02111e-05
AFFX-PheX-M_at 281.595 P 7.00668e-05
AFFX-PheX-3_at 218.748 P 5.16732e-05
AFFX-ThrX-5_at 182.368 P 0.000224668
AFFX-ThrX-M_at 369.629 P 6.02111e-05

Total number of rows: 54675

Table truncated, full table size 1650 Kbytes.

Supplementary file Size Download File type/resource
GSM1131232_10509_614_DMSO_Rep_1_HG-U133_Plus_2_.CEL.gz 5.0 Mb (ftp)(http) CEL
GSM1131232_10509_614_DMSO_Rep_1_HG-U133_Plus_2_.mas5.CHP.gz 484.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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