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Sample GSM1065020 Query DataSets for GSM1065020
Status Public on Mar 02, 2013
Title TAF3 siRNA, no doxorubicin, rep3
Sample type RNA
 
Source name HCT116 cells
Organism Homo sapiens
Characteristics cell line: HCT116 cells
sirna: TAF3 siRNA
treatment: no doxorubicin
Treatment protocol Cells were transfected with control or TAF3 siRNA. 48 hours after siRNA transfection, the cells were treated with 0.5 μM doxorubicin for 24 hours or left untreated.
Growth protocol HCT116 cells were cultured on tissue culture plates in the Dulbecco's Modified Eagle Medium (DMEM, Gibco)
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using the Rneasy kit (Qiagen)
Label biotin
Label protocol Biotinylated cRNA were prepared with the MessageAmp Premier RNA Amplification kit (Applied Biosystems, Foster City, CA). Briefly, 200 ng of total RNA was used to synthesize the first strand of cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer bearing a T7 promoter. The single-stranded cDNA was then converted into a double-stranded DNA (dsDNA) by DNA polymerase I in the presence of E. coli RNase H and DNA ligase. The dsDNA was then served as a template for in vitro transcription in a reaction containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase. The amplified, biotin-labeled antisense RNA (aRNA) was purified and the quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit.
 
Hybridization protocol Standard Illumina hybridization protocol. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization reagents and heated at 65C for 5 min. After cooled to room temperature, total 15 ul of the hybridization solution was applied to Illumina HumanHT-12 v3 chip. The chip was incubated for about 18 hours at 58C. Then washed and stained with streptavidin-Cy3.
Scan protocol Standard Illumina scanning protocol usig Illumina BeadArray Reader. The scanning was done using standard DirectHyb Gene Expression protocol with the following settings: Factor=1, PMT=587, Filter=100%.
Description TAF3 siRNA, no doxorubicin
Illumina HumanHT-12 v3 Beadchip
Data processing Raw data was extracted using Illumina BeadStudio software without normalization. Results were analyzed by GeneSpring GX 10.0.2 using simple median-scaling. Genes were filtered on Flags Present or Marginal.
 
Submission date Jan 16, 2013
Last update date Mar 02, 2013
Contact name Xiaolin Wu
E-mail(s) forestwu@mail.nih.gov
Phone 301-846-7677
Organization name Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc
Department Cancer Research Technology Program
Lab Genomics Laboratory
Street address 8560 Progress Drive, C3001
City Frederick
State/province MD
ZIP/Postal code 21701
Country USA
 
Platform ID GPL6947
Series (2)
GSE43541 H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation [Illumina BeadArray]
GSE43542 H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

Data table header descriptions
ID_REF
VALUE median-scaled signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1802380 524.843 1
ILMN_1893287 72.1672 0.80896
ILMN_1736104 61.8721 0.41765
ILMN_1792389 273.787 0.99868
ILMN_1854015 100.096 0.97892
ILMN_1904757 77.9772 0.90382
ILMN_1740305 87.5588 0.95257
ILMN_1665168 59.2219 0.2635
ILMN_2375156 140.869 0.99209
ILMN_1705423 81.239 0.92754
ILMN_1716072 64.1146 0.53096
ILMN_1697642 524.231 1
ILMN_1788184 72.0652 0.80632
ILMN_1681845 1848.11 1
ILMN_1823296 65.8475 0.6166
ILMN_1889845 77.6715 0.90119
ILMN_1746923 75.327 0.8722
ILMN_1690979 75.327 0.8722
ILMN_1811114 64.1146 0.53491
ILMN_1660729 86.2337 0.94466

Total number of rows: 48803

Table truncated, full table size 1317 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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