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Sample GSM266733 Query DataSets for GSM266733
Status Public on Oct 09, 2008
Title NHP8/DNp53 (Senescent) vs Young NHP8 Cells_rep2
Sample type RNA
 
Channel 1
Source name Young NHP8 cells
Organism Homo sapiens
Characteristics young NHP8 cells at passage-3 (control)
Biomaterial provider Cambrex, Rockland, ME
Growth protocol NHP cells were mostly cultured on collagen-coated dishes in serum/androgen-free, partially defined PrEBM medium containing insulin, EGF, bovine pituitary extract (BPE; Invitrogen, Carlsbad, CA), and antibiotics.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from NHP cells (see Fig. 7A) using an RNeasy
RNA-purification kit (Qiagen, Valencia, CA), including on-column DNase
digestion to completely remove contaminating genomic DNA. RNA
concentrations were determined in NanoDrop and the quality
assessed using a BioAanalyzer.
Label Cy3
Label protocol Labelling was done according to manufacturer's protocol available at
http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
 
Channel 2
Source name NHP8/DNp53 (senescent cells)
Organism Homo sapiens
Characteristics NHP8 cells infected with retrovirus encoding DN(dominant negative)p53 and at passage-6
Biomaterial provider Cambrex, Rockland, ME
Growth protocol NHP cells were mostly cultured on collagen-coated dishes in serum/androgen-free, partially defined PrEBM medium containing insulin, EGF, bovine pituitary extract (BPE; Invitrogen, Carlsbad, CA), and antibiotics.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from NHP cells (see Fig. 7A) using an RNeasy
RNA-purification kit (Qiagen, Valencia, CA), including on-column DNase
digestion to completely remove contaminating genomic DNA. RNA
concentrations were determined in NanoDrop and the quality
assessed using a BioAanalyzer.
Label Cy5
Label protocol Labelling was done according to manufacturer's protocol available at
http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
 
 
Hybridization protocol Manufacturer's protocol available at
http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
Scan protocol Scanning and data acquisition were performed using Agilent scanner and feature extraction protocol GE2-v5_91 (available at www.agilent.com).
Description The current array analysis was carried to study the changes in the gene expression profile of NHP8/DNp53 cells compared to yougn NHP cells.
Data processing The data was acquired using Agilent's feature extraction protocol
GE2-v5_91 with an inbuilt Lowess normalization feature and Logratio
algorithms, for details visit www.agilent.com.
 
Submission date Feb 18, 2008
Last update date Oct 09, 2008
Contact name Dean G Tang
E-mail(s) dtang@mdanderson.org
Organization name U.T M. D. Anderson Cancer Center
Department Carcinogenesis
Lab Dean G Tang's Lab
Street address 1808 Park road 1C
City Smithville
State/province TX
ZIP/Postal code 78957
Country USA
 
Platform ID GPL4133
Series (1)
GSE10570 Normal human prostate (NHP) epithelial cells: Senescent and immortalized cells compared to young progenitors

Data table header descriptions
ID_REF
VALUE LogRatio(base10). Log(REDsignal/GREENsignal) per feature.
PValueLogRatio Significance level of the Log Ratio computed for a feature
gProcessedSignal Cy3 Dye-normalized signal after surrogate algorithm, per channel, used for computation of log ratio.
rProcessedSignal Cy5 Dye-normalized signal after surrogate algorithm, per channel, used for computation of log ratio.
gProcessedSigError Cy3 processed signal error
rProcessedSigError Cy5 processed signal error
gMeanSignal Raw mean signal of feature in green (Cy3) channel
rMeanSignal Raw mean signal of feature in red (Cy5) channel
gBGMeanSignal Mean local (local to corresponding feature) background signal for Cy3
rBGMeanSignal Mean local (local to corresponding feature) background signal for Cy3
gDyeNormSignal Cy3 dye normalized signal
rDyeNormSignal Cy5 dye normalized signal
gDyeNormError The standard error associated with Cy3 dye normalized signal
rDyeNormError The standard error associated with Cy5 dye normalized signal

Data table
ID_REF VALUE PValueLogRatio gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gMeanSignal rMeanSignal gBGMeanSignal rBGMeanSignal gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError
12 -2.87E-01 3.66E-05 4.07E+02 2.10E+02 4.09E+01 2.46E+01 2.03E+02 1.39E+02 4.26E+01 7.51E+01 406.97 210.041 40.8718 24.6038
13 -1.87E-01 3.51E-01 3.55E+01 2.31E+01 5.41E+00 1.21E+01 5.82E+01 8.87E+01 4.21E+01 7.62E+01 35.4561 23.0619 5.40776 12.131
14 -3.12E-01 4.33E-06 1.56E+03 7.63E+02 1.57E+02 7.74E+01 6.53E+02 2.86E+02 4.20E+01 7.75E+01 1564.84 762.597 156.529 77.3535
15 -3.27E-01 3.07E-01 2.34E+01 1.10E+01 5.05E+00 1.10E+01 5.31E+01 8.45E+01 4.18E+01 7.90E+01 23.3525 10.9937 5.05001 10.9892
16 2.20E-01 6.64E-04 2.51E+03 4.17E+03 2.51E+02 4.17E+02 1.02E+03 1.19E+03 4.28E+01 7.97E+01 2512.07 4169.86 251.236 417.189
17 -4.67E-01 5.29E-02 3.35E+01 1.14E+01 5.48E+00 1.00E+01 5.68E+01 8.30E+01 4.22E+01 7.74E+01 33.484 11.4132 5.48412 9.99697
18 -3.43E-02 6.23E-01 1.86E+02 1.72E+02 1.90E+01 2.15E+01 1.17E+02 1.28E+02 4.22E+01 7.73E+01 185.876 171.764 18.9751 21.5328
19 3.62E-02 5.57E-01 3.28E+04 3.56E+04 3.28E+03 3.56E+03 1.34E+04 9.01E+03 4.27E+01 7.67E+01 32771.3 35616.1 3277.13 3561.64
20 -5.45E-01 2.16E-02 4.25E+01 1.21E+01 6.01E+00 1.18E+01 6.02E+01 8.52E+01 4.26E+01 7.78E+01 42.5347 12.1333 6.00764 11.7939
21 -2.50E-01 4.76E-01 1.96E+01 1.10E+01 4.95E+00 1.10E+01 5.19E+01 8.19E+01 4.28E+01 7.62E+01 19.5833 11.0056 4.94973 10.9692
22 -3.00E-01 8.35E-06 6.56E+04 3.29E+04 6.56E+03 3.29E+03 2.72E+04 8.16E+03 4.25E+01 7.64E+01 65555.7 32876.1 6555.57 3287.64
23 -1.27E-01 5.89E-01 2.61E+01 1.95E+01 4.98E+00 1.12E+01 5.46E+01 8.72E+01 4.26E+01 7.50E+01 26.1463 19.5128 4.98382 11.2271
24 -3.56E-01 3.11E-07 2.82E+03 1.24E+03 2.82E+02 1.25E+02 1.14E+03 4.05E+02 4.28E+01 7.74E+01 2818.67 1241.18 281.892 124.827
25 -1.56E-01 1.31E-02 5.87E+04 4.09E+04 5.87E+03 4.09E+03 2.44E+04 1.01E+04 4.21E+01 7.86E+01 58680.3 40935 5868.03 4093.53
26 1.03E-01 4.39E-01 4.38E+01 5.56E+01 5.87E+00 1.40E+01 6.20E+01 9.62E+01 4.15E+01 7.70E+01 43.8468 55.5856 5.87194 13.9819
27 4.43E-01 1.15E-08 1.40E+02 3.89E+02 1.45E+01 4.11E+01 9.97E+01 1.83E+02 4.17E+01 7.77E+01 140.398 389.296 14.5425 41.1143
28 0.00E+00 1.00E+00 5.14E+00 9.82E+00 5.12E+00 9.79E+00 4.45E+01 7.84E+01 4.23E+01 7.63E+01 5.14063 9.82034 5.12296 9.78731
29 0.00E+00 1.00E+00 5.14E+00 9.83E+00 5.12E+00 8.61E+00 4.50E+01 7.96E+01 4.21E+01 7.56E+01 5.13742 9.82767 5.11976 8.614
30 3.09E-01 4.90E-06 2.94E+03 6.00E+03 2.94E+02 6.00E+02 1.19E+03 1.65E+03 4.24E+01 7.60E+01 2943.65 5996.62 294.389 599.81
31 -3.44E-02 9.40E-01 1.15E+01 1.06E+01 4.87E+00 1.06E+01 4.90E+01 8.02E+01 4.22E+01 7.70E+01 11.4972 10.6215 4.87354 10.5858

Total number of rows: 43376

Table truncated, full table size 5411 Kbytes.




Supplementary file Size Download File type/resource
GSM266733.txt.gz 12.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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