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Sample GSM406198 Query DataSets for GSM406198
Status Public on Mar 08, 2010
Title UPF1 and Ago2 siRNA treated Replication 1
Sample type RNA
 
Source name siRNA-treated HeLa cells
Organism Homo sapiens
Characteristics protocol: Ago2/UPF1 knockdown
Treatment protocol Cells were transiently transfected with the indicated in vitro-synthesized siRNA (Invitrogen) using Oligofectamine (Invitrogen) transfection reagent.
Growth protocol HeLa cells were grown in Dulbecco’s Modified Eagle’s Medium (Lonza) containing 10% fetal bovine serum (Lonza).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).
Label biotin
Label protocol Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).
 
Hybridization protocol 750 ng of labeled cRNA samples were hybridized to each human-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).
Scan protocol Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3(Gene Expression Module v3.3.8).
Description replicate 1
Data processing Selected gene signal value was transformed by logarithm and normalized by quantile method. The background correction method was not used to collect the normalized value. Instead, the p-value method was used in which array data with p>0.5 values was removed. Due to all 6 of the samples get rid of p>0.5 gene lists, only 50% of the genes (~12853) could be normalized and give meaningful data. The comparative analysis between Control and Test samples was carried out using fold-change.
 
Submission date May 20, 2009
Last update date Mar 08, 2010
Contact name Junho Choe
E-mail(s) ultimagic@hotmail.com
Organization name School of Life science and Biotechnology
Department korea University
Lab Molecular genomics
Street address Sungbuggu Anam 5ga
City Seoul
ZIP/Postal code 136-701
Country South Korea
 
Platform ID GPL6883
Series (1)
GSE16170 Genome-wide analysis of miRNA-targeted cellular NMD substrates in HeLa cell

Data table header descriptions
ID_REF
VALUE log2, quantile-normalized signal intensity

Data table
ID_REF VALUE
ILMN_1343291 15.94
ILMN_1651209 7.05
ILMN_1651228 11.06
ILMN_1651229 7.78
ILMN_1651237 10.56
ILMN_1651254 10.48
ILMN_1651262 13.85
ILMN_1651268 7.06
ILMN_1651278 9.23
ILMN_1651285 6.91
ILMN_1651286 7.17
ILMN_1651315 12.24
ILMN_1651336 7.29
ILMN_1651346 8.64
ILMN_1651347 10.63
ILMN_1651364 8.20
ILMN_1651378 8.73
ILMN_1651385 10.28
ILMN_1651405 12.60
ILMN_1651429 9.82

Total number of rows: 12853

Table truncated, full table size 229 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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