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Sample GSM384875 Query DataSets for GSM384875
Status Public on Jan 03, 2011
Title EV4, biological rep3
Sample type RNA
 
Source name Human rhabdomyosarcoma cell line
Organism Homo sapiens
Characteristics gender: female
cell type: rhabdomyosarcoma cell
infection: EV71
time: 4 h
Growth protocol Human rhabdomyosarcoma cells (RD) were cultured in MEM medium with 1 mM L-glutamate, 100 units/mL penicillin, 100 £gg/mL streptomycin and 10% fetal bovine serum (Gibco) at 37¢XC, 20% O2 and 5% CO2.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.
Description The mRNA profiles from RD cells infected with/without EV71 were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).
Data processing The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files
 
Submission date Mar 20, 2009
Last update date Jan 03, 2011
Contact name Sung-Liang Yu
E-mail(s) slyu@ntu.edu.tw
Phone 886-2-23958341
Organization name National Taiwan University
Department Clinical Laboratory Sciences and Medical Biotechnology
Lab Microarray Core Facility
Street address Jen Ai Road Section1
City Taipei
ZIP/Postal code 100
Country Taiwan
 
Platform ID GPL570
Series (1)
GSE15323 The differentially expressed genes induced by EV71 infection

Data table header descriptions
ID_REF Affymetrix Synthetic ID
VALUE GC-RMA-calculated Signal intensity

Data table
ID_REF VALUE
1007_s_at 1.057
1053_at 0.864
117_at 0.863
121_at 1.002
1255_g_at 0.693
1294_at 1.106
1316_at 1.001
1320_at 1.021
1405_i_at 0.98
1431_at 0.651
1438_at 0.934
1487_at 1.036
1494_f_at 0.986
1552256_a_at 1.009
1552257_a_at 0.932
1552258_at 0.548
1552261_at 1.001
1552263_at 1.563
1552264_a_at 0.941
1552266_at 0.984

Total number of rows: 54675

Table truncated, full table size 877 Kbytes.




Supplementary file Size Download File type/resource
GSM384875.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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