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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
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TXT
Processed data included within Sample table