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Series GSE4084 Query DataSets for GSE4084
Status Public on Apr 01, 2006
Title Human prostate cancer xenografts on intact mice or after castration.
Platform organism Homo sapiens
Sample organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by array
Summary cDNA expression arrays on a panel of human prostate cancer xenografts. The xenografts can divided into three groups: 1) androgen-dependent, 2) androgen-independent with functional expression of the androgen receptor, 3) androgen-independent lacking functional expression of the androgen receptor. Four microarrays were performed per xenograft using tissue samples collected in separate experiments. Two samples were taken from intact male mice, whereas the other two samples were taken 1 to 2 weeks after castration. The panel of xenografts have been described in van Weerden and Romijn, 2000; Prostate 43:263-71.
Keywords: Different growth characteristics, androgen ablation response
 
Overall design A common reference is used for all hybridizations. This common reference contained two prostate cancer cell lines, Du145 and LNCaP, while the other cell lines originated from breast (MCF7 and ZR75.1), bone (MG63), colon (HT29), endothelium (Ea-hy926), ovary (A2780), skin (SK-MEL-28), B-cell leukemia (Raji), T-cell lymphoblastoma (Jurkat) and fibroblasts (N92-19N and N92-19T).
Xenograft cDNA was always labeled with Cy3; the common reference was always labeled with Cy5.
 
Contributor(s) Hendriksen P, Dits N, van Weerden W, Trapman J, Jenster G
Citation(s) 16707422
Submission date Jan 23, 2006
Last update date Jan 17, 2013
Contact name Peter Hendriksen
E-mail(s) peter.hendriksen@wur.nl
Organization name Wageningen University & Research
Department RIKILT
Street address Akkermaalsbos 2
City Wageningen
ZIP/Postal code 6708 WB
Country Netherlands
 
Platforms (1)
GPL3349 CMF/NKI produced Human 18K cDNA array, spots 1-19200
Samples (52)
GSM92533 PC xenograft PC82 replicate_1
GSM92534 PC xenograft PC82 after castration replicate_1
GSM92535 PC xenograft PC82 replicate_2
Relations
BioProject PRJNA95235

Table 1: PCXenografts, Normal-Castrate, 296 Affected Spots: 296 spots that are affected by castration in at least one prostate cancer xenograft. A cluster picture of these spots is given in figure 1A in Hendriksen et al., Cancer Res 2006; 66(10). This article also provides information about the prostate cancer xenografts. The differences in 2_log ratio between normal and castrated mice (N-C) are given. A positive value means: down-regulated by castration. Spots were considered to be up or down-regulated by castration when the average ratios of two experiments between the intact and castrated mice were larger than 2 (2log 1.0). Additionally, both individual comparisons between xenografts grown on an intact versus castrated mouse had to yield a ratio larger than 1.62 (2log 0.7). header descriptions
ID_REF
AC
X21_PC82_-_X22_PC82Cas
X33_PC82_-_X34_PC82Cas
PC82_N_-_C_AVR
X45_PC295_-_X46_PC295Cas
X47_PC295_-_X48_PC295Cas
PC295_N_-_C_AVR
X13_PC310_-_X14_PC310Cas
X91_PC310_-_X32_PC310Cas
PC310_N_-_C_AVR
X-03_PC346_sept03_-_X04_PC346Cas
X83_PC346_-_X84_PC346Cas
PC346_N_-_C_AVR
X35_PC346B_-_X36_PC346BCas
X87_PC346B_-_X88_PC346BCas
PC346B_N_-_C_AVR
X27_PC346I_-_X28_PC346ICas
X85_PC346I_-_X86_PC346ICas
PC346I_N_-_C_AVR
X19_PC346BI_-_X40_PC346BICas
X89_PC346BI_-_X90_PC346BICas
PC346BI_N_-_C_AVR
X17_PC374_-_X18_PC374Cas
X37_PC374_-_X38_PC374Cas
PC374_N_-_C_AVR
X09_PC133_-_X10_PC133Cas
X41_PC133_-_X42_PC133Cas
PC133_N_-_C_AVR
X11_PC135_-_X12_PC135Cas
X43_PC135_-_X44_PC135Cas
PC135_N_-_C_AVR
X01_PC324_-_X02_PC324Cas
X23_PC324_-_X24_PC324Cas
PC324_N_-_C_AVR
X07_PC339_-_X08_PC339Cas
X29_PC339_-_X30_PC339Cas
PC339_N_-_C_AVR

Data table
ID_REF AC X21_PC82_-_X22_PC82Cas X33_PC82_-_X34_PC82Cas PC82_N_-_C_AVR X45_PC295_-_X46_PC295Cas X47_PC295_-_X48_PC295Cas PC295_N_-_C_AVR X13_PC310_-_X14_PC310Cas X91_PC310_-_X32_PC310Cas PC310_N_-_C_AVR X-03_PC346_sept03_-_X04_PC346Cas X83_PC346_-_X84_PC346Cas PC346_N_-_C_AVR X35_PC346B_-_X36_PC346BCas X87_PC346B_-_X88_PC346BCas PC346B_N_-_C_AVR X27_PC346I_-_X28_PC346ICas X85_PC346I_-_X86_PC346ICas PC346I_N_-_C_AVR X19_PC346BI_-_X40_PC346BICas X89_PC346BI_-_X90_PC346BICas PC346BI_N_-_C_AVR X17_PC374_-_X18_PC374Cas X37_PC374_-_X38_PC374Cas PC374_N_-_C_AVR X09_PC133_-_X10_PC133Cas X41_PC133_-_X42_PC133Cas PC133_N_-_C_AVR X11_PC135_-_X12_PC135Cas X43_PC135_-_X44_PC135Cas PC135_N_-_C_AVR X01_PC324_-_X02_PC324Cas X23_PC324_-_X24_PC324Cas PC324_N_-_C_AVR X07_PC339_-_X08_PC339Cas X29_PC339_-_X30_PC339Cas PC339_N_-_C_AVR
71 AA489100 0.59 1.1 0.85 1.31 0.87 1.09 -0.3 -0.37 -0.33 0.08 -0.24 -0.08 -0.44 -0.15 -0.29 -0.12 0.3 0.09 -0.95 0.13 -0.41 0.15 0.64 0.39 -0.02 -0.8 -0.41 0.17 -0.32 -0.07 -0.44 0.58 0.07 0.4 -0.01 0.19
79 AA479967 0 -0.02 -0.02 -0.95 0.56 -0.2 -0.81 0.53 -0.14 -1.75 -1.1 -1.42 0.02 0.24 0.13 0.26 0.26 0.19 0.01 0.1 -1.63 1.54 -0.04 0.28 1.1 0.69 1.57 1.57 -1.88 -0.61 -1.24 1.61 -0.1 0.76
86 AA252470 -0.73 -1.42 -1.07 -0.54 -0.88 -0.71 -0.38 -0.59 -0.49 -0.94 -0.07 -0.51 0.02 -0.16 -0.07 -0.9 -0.9 -0.62 0.27 -0.18 -0.28 -0.28 -0.12 0.51 0.2 0.19 -0.56 -0.18 0.09 0.16 0.13 0.27 -0.21 0.03
185 AA458994 0.76 0.42 0.59 1.52 2.28 1.9 0.35 1.46 0.91 0.57 0.57 0.25 0.17 0.21 0.17 0.08 0.12 0.15 0.15 -0.09 -0.09 0.02 0.61 0.31 0.7 0.7 0.02 -0.58 -0.28 -0.31 -0.03 -0.17
277 AA625960 0.74 1.61 1.17 0.41 0.8 0.6 0.79 0.72 0.76 0.75 0.66 0.7 0.29 0.25 0.27 0.47 0.26 0.36 0.01 0.06 0.03 -0.34 0.06 -0.14 0.2 -0.14 0.03 0.13 0.08 0.11 0.18 -0.41 -0.12 0.3 -0.26 0.02
667 AA682438 0.33 0.76 0.55 1.61 1.47 1.54 0.5 0.87 0.68 0.16 0.41 0.29 0.35 0.38 0.37 1.16 0.09 0.62 0.71 0.41 0.56 0.26 -0.21 0.03 -0.15 -0.01 -0.08 0.59 0.59 -0.59 0.82 0.12 1.1 0.22 0.66
860 R25377 0.45 0.07 0.26 0.78 1.59 1.19 0.36 0.07 0.22 0.39 0.21 0.3 -0.45 0.09 -0.18 -0.11 0.02 -0.04 0.06 0.11 0.08 0.05 0.07 0.06 0.46 -0.44 0.01 -0.46 -0.46 0.33 0.26 0.3 0.07 0.23 0.15
903 H38799 -0.83 -1.76 -1.3 -1.54 -0.46 -1 -0.41 -0.54 -0.48 -2.3 -0.98 -1.64 -0.3 -0.3 -0.15 -0.13 -0.14 0.06 -0.17 -0.05 -0.72 0.55 -0.08 -0.22 -0.15 -0.19 0.19 0.19 -0.31 0.26 -0.03 -0.16 0.22 0.03
1015 AA101632 0.56 -0.06 0.25 0.17 -0.13 0.02 0 1.32 1.32 1.34 1.43 1.39 0.39 0.36 0.38 0.8 1.01 0.9 1.18 1.18 -0.29 0.17 -0.06 -0.33 0.11 -0.11 -0.42 -0.42 -0.36 0.28 -0.04 -0.04 0.09 0.03
1064 AA465697 1.01 1.18 1.1 -1.15 -0.7 -0.93 0.27 0.53 0.4 0.33 0.48 0.41 0.04 -0.42 -0.19 -0.03 0.07 0.02 -0.01 0.1 0.04 -0.1 -0.15 -0.13 -0.01 0.22 0.1 -0.57 -0.57 -0.32 0.27 -0.03 0.52 0.37 0.45
1100 AA155913 0 0 0 -0.46 0 -0.46 0 0 0 3.64 2.58 3.11 -0.33 -0.33 1.72 1.72 0.68 -0.12 0.28 -0.25 -0.25 0.26 0.26
1453 AA426113 0 0.86 0.86 0.98 1.97 1.47 0 0.55 0.55 0.24 0.24 -0.12 0.14 0.01 0.41 0.56 0.49 -0.06 0.22 0.08 0.41 0.24 0.33 -0.33 0.52 0.1 0.26 -0.23 0.01
1526 H72122 -0.03 0 -0.03 -0.32 -0.07 -0.19 0 0 0 -1.12 -0.92 -1.02 -1.2 -0.24 -0.72 -0.41 -0.41 0.09 0.09 0.42 0.93 0.67
1577 W68220 0 1.42 1.42 0.73 1.9 1.31 0 1.66 1.66 0.84 0.21 0.53 0.3 0.57 0.44 0.47 0.01 0.24 0.37 0.17 0.27 -0.16 -0.19 -0.18 -0.22 1.09 0.43 0.38 0.28 0.33 -0.1 0.51 0.21 0.07 0.19 0.13
1687 AA131299 0.07 0.79 0.43 -0.49 -0.97 -0.73 -0.39 -1.78 -1.09 -2.16 -0.82 -1.49 0.16 -0.12 0.02 0.1 0.2 0.15 -0.36 0.26 -0.05 0.48 0.12 0.3 0.02 -0.61 -0.3 -0.49 0.32 -0.08 -0.09 0.13 0.02 0.13 0.4 0.27
1761 H15416 1.17 1.04 1.11 0 0.96 0.96 0 0 0 0.34 0.34 -0.3 -0.3 1.29 0.19 0.74 0.11 -0.08 0.01 -0.11 0.34 0.12 0.93 0.93 -0.38 -0.38
1767 AA400292 -0.49 -0.51 -0.5 -1.06 -1.16 -1.11 -1.39 -1.03 -1.21 -0.93 -0.66 -0.79 -0.65 -0.36 -0.51 -0.48 0.1 -0.19 0.46 0.09 0.28 0.36 -0.04 0.16 -0.17 -0.41 -0.29 0.15 0.84 0.5 -1.71 -0.06 -0.89 -0.58 0.53 -0.03
1780 H28091 -1.05 0.24 -0.4 -1.36 -1.53 -1.44 -1.34 -0.48 -0.91 -1.42 -0.66 -1.04 0.01 -0.31 -0.15 -0.18 0.14 -0.02 -0.12 -0.12 -0.12 0.09 0.7 0.39 -0.07 -0.46 -0.27 -0.54 -0.9 -0.72 -1.32 -0.46 -0.89 1.51 0.25 0.88
1827 AA504348 0.49 0.85 0.67 0 1.95 1.95 1.41 1.71 1.56 0.06 0.27 0.16 0.07 0.05 0.06 -0.45 0.13 -0.16 -0.23 0.12 -0.05 0.27 -0.24 0.02 0.16 -0.22 -0.03 -0.05 -0.05 0.07 -0.07 0 -0.11 -0.04 -0.07
2052 AA455942 -0.11 -0.23 -0.17 0.35 -0.23 0.06 -1.06 -1.52 -1.29 0.06 -0.12 -0.03 -0.3 -0.09 -0.19 -0.46 0.14 -0.16 -0.88 -0.17 -0.52 -0.27 -0.03 -0.15 0.22 -0.03 0.09 -0.11 -0.42 -0.27 -0.28 0.06 -0.11 0.41 0.26 0.33

Total number of rows: 296

Table truncated, full table size 55 Kbytes.




Table 2: PCXenografts, Normal-Castrate, All Spots: The differences in 2_log ratio of prostate cancer xenografts collected from intact mice (N) vs. those collected 7 to 14 days after castration (C). A positive value means: down-regulated by castration. The calculations are based on the averages of 2 N_vs._C comparisons, thus 4 arrays per xenograft. The expression values of the individual arrays are also provided in GEO. More information, for example about the xenografts, is provided in Hendriksen et al., Cancer Res 2006; 66(10). header descriptions
ID_REF
AC
PC82_N_-_C_2LR
PC295_N_-_C_2LR
PC310_N_-_C_2LR
PC346_N_-_C_2LR
PC346B_N_-_C_2LR
PC346I_N_-_C_2LR
PC346BI_N_-_C_2LR
PC374_N_-_C_2LR
PC133_N_-_C_2LR
PC135_N_-_C_2LR
PC324_N_-_C_2LR
PC339_N_-_C_2LR

Data table
ID_REF AC PC82_N_-_C_2LR PC295_N_-_C_2LR PC310_N_-_C_2LR PC346_N_-_C_2LR PC346B_N_-_C_2LR PC346I_N_-_C_2LR PC346BI_N_-_C_2LR PC374_N_-_C_2LR PC133_N_-_C_2LR PC135_N_-_C_2LR PC324_N_-_C_2LR PC339_N_-_C_2LR
1 W96463 -0.01 -0.11 0.2 0.38 0.03 -0.36 0.7 0.21 0.33 0.1 0.12 -0.01
2 N51917 0.05 0.17 -0.25 0.14 -0.14 0.31 0.3 0.03 -0.05 -0.11 0 0.27
3 AA056580 -0.17 0 -0.04 -0.17 -0.25 -0.75 0.22 0.3 0.4 0.75 0.06 0.15
4 AA129861 -0.11 0.04 -0.2 0.05 0 0.14 0.49 0.01 0.07 0.13 0.08 -0.1
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

Total number of rows: 19200

Table truncated, full table size 1034 Kbytes.




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