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Sample GSM266720 Query DataSets for GSM266720
Status Public on Oct 09, 2008
Title NHP8 near senescent/senescent vs young_rep1
Sample type RNA
 
Channel 1
Source name Normal human prostate (NHP8) young 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 near senescent/senescent cells
Organism Homo sapiens
Characteristics NHP8 cells at passage-5
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 was 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 profiles of near senescent NHP cells compared to young 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 1.70E-02 7.89E-01 3.48E+02 3.62E+02 3.55E+01 3.79E+01 1.88E+02 5.64E+02 4.11E+01 9.11E+01 348.262 362.141 35.4844 37.8859
13 -2.91E-01 4.40E-01 2.07E+01 1.06E+01 7.68E+00 1.06E+01 6.07E+01 1.43E+02 4.08E+01 8.96E+01 20.7166 10.6102 7.67635 10.5891
14 -5.13E-01 3.93E-11 1.56E+03 4.77E+02 1.56E+02 4.91E+01 6.42E+02 6.73E+02 4.07E+01 9.00E+01 1555.61 476.911 155.715 49.0876
15 -1.97E-01 6.42E-01 1.70E+01 1.08E+01 7.86E+00 1.08E+01 5.88E+01 1.25E+02 4.10E+01 8.80E+01 17.0305 10.829 7.85986 10.7868
16 4.31E-01 3.62E-09 2.52E+03 6.80E+03 2.52E+02 6.80E+02 9.98E+02 7.49E+03 4.09E+01 8.45E+01 2519.78 6799.06 252.075 680.015
17 0.00E+00 1.00E+00 9.77E+00 1.08E+01 8.14E+00 1.08E+01 5.58E+01 1.09E+02 4.05E+01 8.48E+01 9.76882 10.8077 8.14482 10.7656
18 3.10E-01 1.70E-05 1.71E+02 3.48E+02 1.86E+01 3.69E+01 1.13E+02 5.09E+02 4.08E+01 8.60E+01 170.828 348.49 18.6149 36.871
19 8.03E-03 8.96E-01 3.03E+04 3.08E+04 3.03E+03 3.08E+03 1.19E+04 3.01E+04 4.07E+01 8.60E+01 30257.6 30822.6 3025.77 3082.29
20 -1.09E-01 7.16E-01 2.39E+01 1.86E+01 8.17E+00 1.20E+01 6.01E+01 1.46E+02 4.05E+01 8.22E+01 23.8925 18.5947 8.16596 12.0291
21 0.00E+00 1.00E+00 8.50E+00 1.12E+01 8.48E+00 1.12E+01 5.36E+01 1.09E+02 4.07E+01 8.37E+01 8.49785 11.2069 8.4843 11.1633
22 -2.68E-01 5.02E-05 6.82E+04 3.68E+04 6.82E+03 3.68E+03 2.66E+04 3.40E+04 4.10E+01 8.40E+01 68175.2 36766.8 6817.53 3676.7
23 0.00E+00 1.00E+00 8.62E+00 1.14E+01 8.59E+00 1.14E+01 5.23E+01 1.03E+02 4.06E+01 8.22E+01 8.62125 11.4187 8.59218 11.3742
24 -2.68E-01 5.24E-05 3.15E+03 1.70E+03 3.15E+02 1.70E+02 1.14E+03 1.83E+03 4.14E+01 8.31E+01 3146.76 1699.08 314.767 170.408
25 -6.37E-01 6.51E-14 3.62E+04 8.35E+03 3.62E+03 8.35E+02 1.31E+04 8.08E+03 4.11E+01 8.26E+01 36198.4 8346.37 3619.84 834.751
26 5.23E-01 1.49E-06 4.48E+01 1.49E+02 9.04E+00 1.98E+01 6.62E+01 2.69E+02 4.06E+01 8.31E+01 44.7878 149.472 9.041 19.7818
27 4.93E-01 3.23E-09 1.06E+02 3.31E+02 1.33E+01 3.55E+01 8.62E+01 4.51E+02 4.13E+01 8.24E+01 106.236 330.66 13.2577 35.5205
28 0.00E+00 1.00E+00 8.85E+00 1.18E+01 8.82E+00 1.18E+01 4.96E+01 1.00E+02 4.03E+01 8.29E+01 8.85287 11.8452 8.82003 11.7991
29 0.00E+00 1.00E+00 8.89E+00 1.19E+01 8.85E+00 1.19E+01 4.85E+01 9.39E+01 4.12E+01 8.38E+01 8.88737 11.9145 8.8544 11.8681
30 1.42E-01 2.41E-02 2.57E+03 3.56E+03 2.57E+02 3.57E+02 9.15E+02 3.57E+03 4.14E+01 8.58E+01 2572.25 3564.07 257.343 356.665
31 0.00E+00 1.00E+00 8.95E+00 1.20E+01 8.91E+00 1.20E+01 4.82E+01 9.64E+01 4.08E+01 8.24E+01 8.94687 12.0407 8.91368 11.9939

Total number of rows: 43376

Table truncated, full table size 5409 Kbytes.




Supplementary file Size Download File type/resource
GSM266720.txt.gz 13.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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