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Status
Public on Oct 09, 2008
Title
NHP8/p16sh (near 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
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/p16sh (near senescent) cells
Organism
Homo sapiens Characteristics
NHP8 cells infected with retrovirus encoding p16 small hairpin RNA and at passage-9
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
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/p16sh (near-senescent) cells compared to young NHP cells.
Data processing
The data was acquired using Agilent's feature extraction protocol
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
6.39E-02
3.03E-01
4.20E+02
4.86E+02
4.23E+01
4.88E+01
1.94E+02
6.33E+02
4.28E+01
7.39E+01
419.532
485.998
42.2565
48.8044
13
-2.72E-02
8.20E-01
2.94E+01
2.76E+01
5.88E+00
5.15E+00
5.74E+01
1.14E+02
4.26E+01
7.36E+01
29.3527
27.5738
5.88357
5.1507
14
-4.54E-01
9.47E-10
1.81E+03
6.34E+02
1.81E+02
6.36E+01
7.02E+02
8.04E+02
4.27E+01
7.40E+01
1805.94
634.195
180.661
63.5752
15
-3.21E-01
4.93E-02
2.73E+01
1.30E+01
5.66E+00
4.51E+00
5.71E+01
9.70E+01
4.29E+01
7.39E+01
27.269
13.0354
5.6643
4.50949
16
4.29E-01
4.16E-09
2.73E+03
7.32E+03
2.73E+02
7.32E+02
1.08E+03
8.37E+03
4.25E+01
7.42E+01
2729.54
7323.69
272.994
732.383
17
1.67E-01
7.16E-01
5.06E+00
7.43E+00
4.75E+00
4.46E+00
4.93E+01
9.05E+01
4.26E+01
7.52E+01
5.05777
7.42665
4.74533
4.4613
18
2.59E-01
1.08E-04
1.78E+02
3.22E+02
1.84E+01
3.25E+01
1.12E+02
4.72E+02
4.28E+01
7.52E+01
177.679
322.377
18.4245
32.5089
19
1.47E-01
1.94E-02
3.95E+04
5.55E+04
3.95E+03
5.55E+03
1.53E+04
6.43E+04
4.28E+01
7.61E+01
39534.1
55454.1
3953.41
5545.41
20
1.47E-01
4.12E-01
1.38E+01
1.93E+01
4.96E+00
4.60E+00
5.27E+01
1.06E+02
4.32E+01
7.43E+01
13.7545
19.3053
4.95898
4.59886
21
-2.42E-01
6.13E-01
7.50E+00
4.30E+00
4.64E+00
4.30E+00
5.06E+01
8.59E+01
4.37E+01
7.60E+01
7.50499
4.30199
4.64037
4.29622
22
-8.95E-02
1.49E-01
7.98E+04
6.49E+04
7.98E+03
6.49E+03
3.11E+04
7.77E+04
4.31E+01
7.78E+01
79799.6
64939.4
7979.96
6493.94
23
1.69E-01
7.30E-01
4.54E+00
6.69E+00
4.53E+00
4.29E+00
4.91E+01
9.06E+01
4.24E+01
7.41E+01
4.53749
6.68944
4.53442
4.29131
24
-2.12E-01
9.78E-04
3.28E+03
2.01E+03
3.28E+02
2.01E+02
1.34E+03
2.50E+03
4.28E+01
7.45E+01
3276.43
2009.15
327.674
200.959
25
-3.50E-01
4.35E-07
7.59E+04
3.39E+04
7.59E+03
3.39E+03
3.03E+04
4.08E+04
4.31E+01
7.47E+01
75923.6
33906.4
7592.36
3390.65
26
3.23E-01
3.53E-05
4.73E+01
9.94E+01
6.68E+00
1.07E+01
6.58E+01
2.11E+02
4.30E+01
7.40E+01
47.2568
99.3988
6.67838
10.6919
27
3.19E-01
3.67E-06
1.69E+02
3.51E+02
1.75E+01
3.53E+01
1.13E+02
5.30E+02
4.36E+01
7.57E+01
168.539
350.995
17.478
35.3239
28
0.00E+00
1.00E+00
4.40E+00
4.19E+00
4.38E+00
4.17E+00
4.50E+01
8.28E+01
4.37E+01
7.55E+01
4.39525
4.18682
4.37966
4.17128
29
0.00E+00
1.00E+00
4.38E+00
4.17E+00
4.36E+00
4.16E+00
4.45E+01
7.74E+01
4.34E+01
7.75E+01
4.37836
4.17154
4.36284
4.15606
30
1.98E-01
1.95E-03
3.89E+03
6.15E+03
3.89E+02
6.15E+02
1.64E+03
7.60E+03
4.29E+01
7.42E+01
3892.21
6145.09
389.245
614.523
31
0.00E+00
1.00E+00
4.35E+00
4.15E+00
4.34E+00
4.13E+00
4.87E+01
7.85E+01
4.37E+01
7.44E+01
4.34921
4.14528
4.33564
4.1299
43376 5410 Kbytes .Supplementary file Size Download File type/resource GSM266736.txt.gz
12.9 Mb
(ftp) (http) TXT
Processed data included within Sample table
