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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 athttp://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 athttp://www.chem.agilent.com/temp/rad71A57/00001389.PDF
Hybridization protocol
Manufacturer's protocol available athttp://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
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TXT
Processed data included within Sample table