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Sample GSM307629 Query DataSets for GSM307629
Status Public on Jun 30, 2009
Title lacZ transfected HCT116-3(6), replicate 8
Sample type RNA
 
Channel 1
Source name Human HCT116-3(6) cells lacZ transfected, untreated
Organism Homo sapiens
Characteristics Human HCT116-3(6) cells lacZ transfected, untreated
Extracted molecule total RNA
Extraction protocol Total RNA from HCT116-3(6) cells transiently transfected with lacZ siRNA oligo without treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.
Label Cy3
Label protocol Total RNA were converted to cRNA, labeled with Cy3 dUTP using Agilent Low Input Linear RNA Amplification, and hybridized to the Phalanx Human One array
 
Channel 2
Source name Human HCT116-3(6) cells lacZ transfected, HU treated
Organism Homo sapiens
Characteristics Human HCT116-3(6) cells lacZ transfected, HU treated
Extracted molecule total RNA
Extraction protocol Total RNA from HCT116-3(6) cells transiently transfected with lacZ siRNA oligo with treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.
Label Cy5
Label protocol Total RNA were converted to cRNA, labeled with Cy5 dUTP using Agilent Low Input Linear RNA Amplification, and hybridized to the Phalanx Human One array
 
 
Hybridization protocol standard hybridization procedure
Scan protocol After hybridization, the slides were scanned with Axon 4000B, and the raw data were generated by Genepix 6.0.
Description Four biological repeats were performed for each condition (-HU or +HU), with two technical repeats (dye swap) per biological sample.
Data processing The data was normalized with quantile normalization of DNAMR (http://www.rci.rutgers.edu/~cabrera/DNAMR), and fitted with the linear model from the R package Limma (Smyth, 2004).
 
Submission date Jul 24, 2008
Last update date Jun 30, 2009
Contact name Vera Huang
E-mail(s) vera324@yahoo.com
Organization name UCSD-Moores Cancer Center
Department Medicine
Lab Jean Wang Lab
Street address 3855 Health Science Drive, Room 4317
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL6254
Series (1)
GSE12242 Gene expression profiling in p53 and p73 double knockdown HCT116-3(6) cells

Data table header descriptions
ID_REF
R6039 normalized Cy5 signal
G6039 normalized Cy3 signal
VALUE normalized log2 ratio (HU/untreated)

Data table
ID_REF R6039 G6039 VALUE
PH_hs_0004877 10.95777486 10.99916041 -0.005438536
PH_hs_0033433 7.257357027 6.953445298 0.061716263
PH_hs_0026582 7.184662351 7.550125839 -0.071580332
PH_hs_0035481 9.234215323 9.299200749 -0.010117351
PH_hs_0023317 6.832834507 6.303780748 0.116266827
PH_hs_0025134 7.900854179 7.383704292 0.097663859
PH_hs_0023499 9.784137543 8.871897843 0.141201932
PH_hs_0025293 7.703866238 7.223929052 0.09279893
PH_hs_0023725 7.643838156 7.577112387 0.012649086
PH_hs_0040748 6.531191746 6.294591484 0.053233514
PH_hs_0032109 7.542404194 7.038073764 0.099843831
PH_hs_0010306 6.73469372 6.965045246 -0.048520388
PH_hs_0001352 6.86406655 6.870153907 -0.001278879
PH_hs_0022361 6.531191746 6.679462935 -0.032385843
PH_hs_0014165 10.5664105 10.20573067 0.05010589
PH_hs_0032993 6.693470123 6.599836172 0.020324134
PH_hs_0021034 12.69382507 12.22063727 0.054807347
PH_hs_0011065 11.11705522 10.92252236 0.025468625
PH_hs_0041074 6.800885394 6.55450721 0.053235263
PH_hs_0004580 6.499647694 6.679462935 -0.039370586

Total number of rows: 30932

Table truncated, full table size 1512 Kbytes.




Supplementary file Size Download File type/resource
GSM307629.gpr.gz 4.0 Mb (ftp)(http) GPR
Processed data included within Sample table

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