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Status
Public on Oct 09, 2008
Title
NHP8/DNp53 (Senescent) vs Young NHP8 Cells_rep1
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/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
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
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
-2.26E-01
1.16E-03
3.61E+02
2.15E+02
3.63E+01
2.67E+01
1.86E+02
1.33E+02
4.08E+01
8.12E+01
361.273
214.645
36.3445
26.7483
13
-7.83E-02
7.94E-01
2.32E+01
1.94E+01
5.23E+00
1.37E+01
5.29E+01
8.85E+01
4.05E+01
7.87E+01
23.2361
19.4015
5.23242
13.6895
14
-3.30E-01
1.64E-06
1.57E+03
7.36E+02
1.57E+02
7.53E+01
6.57E+02
2.53E+02
4.11E+01
7.74E+01
1571.43
735.828
157.193
75.3233
15
-3.38E-01
2.75E-01
2.93E+01
1.34E+01
5.60E+00
1.34E+01
5.47E+01
8.06E+01
4.11E+01
7.88E+01
29.2663
13.4247
5.60015
13.3724
16
2.17E-01
7.76E-04
2.36E+03
3.88E+03
2.36E+02
3.89E+02
9.55E+02
9.86E+02
4.14E+01
7.99E+01
2355.01
3882.15
235.535
388.545
17
-1.66E-01
6.19E-01
1.87E+01
1.28E+01
5.37E+00
1.06E+01
5.11E+01
8.64E+01
4.14E+01
8.01E+01
18.7186
12.7811
5.36794
10.6483
18
-1.57E-01
3.44E-02
1.72E+02
1.20E+02
1.77E+01
1.71E+01
1.11E+02
1.11E+02
4.11E+01
7.92E+01
172.152
120.051
17.6853
17.1491
19
9.26E-03
8.80E-01
3.31E+04
3.38E+04
3.31E+03
3.38E+03
1.35E+04
7.53E+03
4.19E+01
7.88E+01
33057.5
33770.1
3305.75
3377.05
20
5.93E-02
7.34E-01
3.88E+01
4.45E+01
5.77E+00
1.57E+01
5.94E+01
9.40E+01
4.12E+01
7.98E+01
38.8117
44.4904
5.76947
15.6821
21
-1.07E-01
7.57E-01
1.61E+01
1.25E+01
5.39E+00
9.98E+00
5.02E+01
8.52E+01
4.12E+01
7.96E+01
16.0547
12.5397
5.38551
9.97955
22
-3.30E-01
1.45E-06
6.68E+04
3.12E+04
6.68E+03
3.12E+03
2.75E+04
6.87E+03
4.14E+01
7.74E+01
66758.6
31242.5
6675.86
3124.3
23
-4.27E-01
1.14E-01
3.66E+01
1.37E+01
5.00E+00
1.36E+01
5.75E+01
8.22E+01
4.11E+01
7.86E+01
36.6466
13.6983
5.0001
13.6449
24
-3.65E-01
1.87E-07
2.79E+03
1.20E+03
2.79E+02
1.21E+02
1.12E+03
3.63E+02
4.09E+01
8.06E+01
2790.51
1204.25
279.08
121.488
25
-1.84E-01
3.92E-03
5.67E+04
3.72E+04
5.67E+03
3.72E+03
2.34E+04
8.17E+03
4.19E+01
8.06E+01
56734.1
37169.7
5673.41
3717.01
26
4.01E-03
9.81E-01
3.57E+01
3.61E+01
5.63E+00
1.26E+01
5.82E+01
9.20E+01
4.16E+01
7.68E+01
35.721
36.0524
5.63099
12.6432
27
3.85E-01
5.86E-07
1.46E+02
3.54E+02
1.51E+01
3.87E+01
1.01E+02
1.66E+02
4.09E+01
7.82E+01
145.869
353.691
15.1389
38.748
28
0.00E+00
1.00E+00
8.06E+00
1.15E+01
5.63E+00
1.15E+01
4.78E+01
8.15E+01
4.11E+01
7.91E+01
8.05926
11.538
5.63221
11.4931
29
0.00E+00
1.00E+00
5.82E+00
1.11E+01
5.79E+00
1.11E+01
4.44E+01
8.19E+01
4.13E+01
7.70E+01
5.81588
11.0936
5.79483
11.0504
30
2.84E-01
2.08E-05
3.09E+03
5.94E+03
3.09E+02
5.95E+02
1.22E+03
1.48E+03
4.08E+01
7.83E+01
3091.89
5944.39
309.216
594.65
31
-2.07E-01
5.74E-01
2.06E+01
1.28E+01
5.42E+00
1.28E+01
5.19E+01
8.59E+01
4.08E+01
7.85E+01
20.6317
12.8104
5.42209
12.7997
43376 5411 Kbytes .Supplementary file Size Download File type/resource GSM266732.txt.gz
12.9 Mb
(ftp) (http) TXT
Processed data included within Sample table
