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Status
Public on Oct 09, 2008
Title
NHP8/hTERT (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
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/hTERT (senescent) cells
Organism
Homo sapiens Characteristics
NHP8 cells infected with retrovirus encoding hTERT 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
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 profile of NHP8/hTERT (senescent) cells compared to young NHP cells.
Data processing
The data was acquired using Agilent's feature extraction protocol GE2-v5_91 with 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
-2.45E-01
2.13E-04
4.90E+02
2.79E+02
4.93E+01
2.89E+01
1.79E+02
2.00E+02
4.41E+01
7.60E+01
490.034
278.603
49.2561
28.8678
13
-3.96E-01
1.86E-02
3.39E+01
1.36E+01
5.02E+00
6.99E+00
5.51E+01
8.79E+01
4.33E+01
7.71E+01
33.8573
13.6007
5.02449
6.99234
14
-2.82E-01
2.36E-05
2.09E+03
1.09E+03
2.09E+02
1.09E+02
6.25E+02
5.46E+02
4.38E+01
7.71E+01
2086.5
1090.46
208.706
109.308
15
7.34E-02
5.77E-01
2.67E+01
3.17E+01
4.50E+00
7.60E+00
5.37E+01
9.63E+01
4.35E+01
7.65E+01
26.7368
31.6632
4.50134
7.5987
16
3.55E-01
3.33E-07
3.36E+03
7.60E+03
3.36E+02
7.60E+02
9.83E+02
3.37E+03
4.37E+01
7.53E+01
3357.78
7597.72
335.812
759.809
17
-2.35E-01
6.01E-01
1.07E+01
6.21E+00
5.85E+00
6.20E+00
4.94E+01
8.39E+01
4.32E+01
7.70E+01
10.6721
6.20791
5.8515
6.20401
18
-9.33E-02
1.51E-01
2.19E+02
1.77E+02
2.25E+01
1.91E+01
1.08E+02
1.60E+02
4.33E+01
7.58E+01
219.321
176.919
22.4663
19.1124
19
8.59E-02
1.65E-01
4.18E+04
5.09E+04
4.18E+03
5.09E+03
1.27E+04
2.11E+04
4.34E+01
7.60E+01
41757.1
50891.4
4175.71
5089.15
20
3.01E-01
2.53E-03
3.09E+01
6.19E+01
4.45E+00
9.23E+00
5.54E+01
1.11E+02
4.37E+01
7.61E+01
30.9239
61.8572
4.45215
9.2258
21
-3.63E-01
3.38E-01
1.42E+01
6.16E+00
5.75E+00
6.14E+00
5.06E+01
7.99E+01
4.33E+01
7.71E+01
14.2109
6.15943
5.74616
6.13759
22
-1.98E-01
2.01E-03
8.91E+04
5.65E+04
8.91E+03
5.65E+03
2.82E+04
2.31E+04
4.39E+01
7.87E+01
89131.9
56533
8913.19
5653.31
23
-3.72E-01
2.82E-01
1.44E+01
6.10E+00
4.68E+00
6.09E+00
5.08E+01
8.24E+01
4.38E+01
7.76E+01
14.3628
6.10435
4.67689
6.08597
24
-2.05E-01
1.38E-03
3.87E+03
2.41E+03
3.87E+02
2.41E+02
1.18E+03
1.16E+03
4.36E+01
7.68E+01
3873.48
2413.47
387.376
241.454
25
-3.55E-01
3.21E-07
8.03E+04
3.54E+04
8.03E+03
3.54E+03
2.52E+04
1.50E+04
4.45E+01
7.57E+01
80271.1
35428.3
8027.11
3542.84
26
4.58E-01
1.79E-07
4.37E+01
1.26E+02
6.51E+00
1.43E+01
5.97E+01
1.41E+02
4.34E+01
7.64E+01
43.7221
125.651
6.50738
14.2833
27
4.12E-01
1.59E-08
2.04E+02
5.27E+02
2.09E+01
5.31E+01
1.07E+02
3.23E+02
4.31E+01
7.54E+01
204.039
526.836
20.9227
53.1489
28
0.00E+00
1.00E+00
5.67E+00
5.73E+00
5.65E+00
5.71E+00
4.50E+01
7.59E+01
4.35E+01
7.46E+01
5.67128
5.72891
5.6522
5.7086
29
0.00E+00
1.00E+00
5.65E+00
5.71E+00
5.64E+00
5.69E+00
4.69E+01
8.05E+01
4.35E+01
7.57E+01
5.65457
5.7091
5.63554
5.68885
30
3.40E-01
7.89E-07
3.99E+03
8.72E+03
3.99E+02
8.72E+02
1.23E+03
4.10E+03
4.33E+01
7.63E+01
3987.48
8724.41
398.774
872.469
31
0.00E+00
1.00E+00
5.62E+00
5.67E+00
4.51E+00
5.67E+00
4.84E+01
8.33E+01
4.30E+01
7.62E+01
5.6234
5.67275
4.51063
5.66606
43376 5411 Kbytes .Supplementary file Size Download File type/resource GSM266730.txt.gz
12.9 Mb
(ftp) (http) TXT
Processed data included within Sample table
