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Sample GSM200010 Query DataSets for GSM200010
Status Public on Dec 17, 2007
Title 1_040206 Hog1+hog2 hog2cy5+hog1cy3 2389 CK-TEST
Sample type RNA
 
Channel 1
Source name test
Organism Sus scrofa
Characteristics The RNA was isolated from back fat tissue of Chinese Miniature pigs, which was 3 month-old hog.
Treatment protocol The pig was fed with clenbuterol.
Growth protocol Eight Chinese miniature pigs were used in the experiments. Four hogs and four sows, all 4 weeks old, were housed in the Nutrition and Metabolism Laboratory at the China Agriculture University. They were raised under exactly the same conditions and were fed the same diets until 8 weeks (average body weight 17 kg). They were randomly divided into 4 groups with each group having two pigs with the same gender and the same parents. For the following 4 weeks, one pig in each group was fed 25 mg/kg clenbuterol twice daily in their diets as the test pig, while the other was fed the same diet without clenbuterol as the control. Then one group of hogs and one group of sows were slaughtered for analysis. These two groups are referred to as the 3 month-old pigs. The other two groups were fed with/without 50 mg/kg clenbuterol twice daily in their diets for another 4 weeks and slaughtered for analysis. These two groups are referred to as the 4 month-old pigs. Approximately 1 g biopsies were taken from the back fat adipose tissues (at the fifth lumbar vertebra level) of each pig. The adipose tissue samples were washed in sterile water, snap frozen in liquid nitrogen and stored at -80℃.
Extracted molecule total RNA
Extraction protocol Total RNA of the adipose tissue was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD, USA) and further purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufacturers instructions.
Label cy3
Label protocol Reverse transcription was done with 10 µg total RNA as the template to synthesize cDNA incorporated with flourence dye Cy3-dCTP or Cy5-dCTP. Probes were purified on a Qiagen spin column (Qiagen, Valencia, CA, USA). Mix dye-labeled cDNA together and dry dye-labeled cDNA were used for hybridization.
 
Channel 2
Source name control
Organism Sus scrofa
Characteristics The RNA was isolated from back fat tissue of Chinese Miniature pigs, which was 3 month-old hog.
Treatment protocol The pig was fed without clenbuterol.
Growth protocol Eight Chinese miniature pigs were used in the experiments. Four hogs and four sows, all 4 weeks old, were housed in the Nutrition and Metabolism Laboratory at the China Agriculture University. They were raised under exactly the same conditions and were fed the same diets until 8 weeks (average body weight 17 kg). They were randomly divided into 4 groups with each group having two pigs with the same gender and the same parents. For the following 4 weeks, one pig in each group was fed 25 mg/kg clenbuterol twice daily in their diets as the test pig, while the other was fed the same diet without clenbuterol as the control. Then one group of hogs and one group of sows were slaughtered for analysis. These two groups are referred to as the 3 month-old pigs. The other two groups were fed with/without 50 mg/kg clenbuterol twice daily in their diets for another 4 weeks and slaughtered for analysis. These two groups are referred to as the 4 month-old pigs. Approximately 1 g biopsies were taken from the back fat adipose tissues (at the fifth lumbar vertebra level) of each pig. The adipose tissue samples were washed in sterile water, snap frozen in liquid nitrogen and stored at -80℃.
Extracted molecule total RNA
Extraction protocol Total RNA of the adipose tissue was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD, USA) and further purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufacturers instructions.
Label cy5
Label protocol Reverse transcription was done with 10 µg total RNA as the template to synthesize cDNA incorporated with flourence dye Cy3-dCTP or Cy5-dCTP. Probes were purified on a Qiagen spin column (Qiagen, Valencia, CA, USA). Mix dye-labeled cDNA together and dry dye-labeled cDNA were used for hybridization.
 
 
Hybridization protocol See Pronto Universal hybridization kit Quick Reference Guide.
Scan protocol Arrays were scanned with a ScanArray Express scanner (Parckard Bioscience, Kanata, OT，USA) with the obtained images analyzed with GenePix Pro 4.0 (Axon Instruments, Foster City, CA ) and Acuity 4.0 (Axon Instruments, Foster City, CA).
Description To avoid dye bias, the experiments were performed in duplicate by dye swap with Cy5-dCTP first used with the test pig and Cy3-dCTP used with the control pig and then Cy3-dCTP used with the test pig and Cy5-dCTP used with the control pig.
Data processing The resulting microarray data was then normalized using the space and intensity-dependent normalization in the LOWESS program [40]. Each gene was represented in triplicate on each slide. The intensity (median) of each spot was analyzed using the student t-test to identify the differentially expressed genes (P<0.05). Low quality spots were filtered out before the student t-test analysis. Low spots refer to stained spots with bad images or spots with the intensities (median) lower than 200 (too weak) or greater than 60000 (saturated).
 
Submission date Jun 10, 2007
Last update date Aug 14, 2011
Contact name Jin Zhang
E-mail(s) zhangjin7688@163.com
Organization name China Agricultural University
Street address 2#, Yuanmingyuan West Road
City Beijing
ZIP/Postal code 100094
Country China
 
Platform ID GPL5374
Series (1)
GSE8093 Differential Gene Expression Profile in Pig Adipose Tissue Treated with/without Clenbuterol

Data table header descriptions
ID_REF
VALUE Log Ratio(test/control) with flagged values removed
F635 Median
F635 Mean
F635 SD
B635 Median
B635 Mean
B635 SD
% > B635+1SD
% > B635+2SD
F635 % Sat.
F532 Median
F532 Mean
F532 SD
B532 Median
B532 Mean
B532 SD
% > B532+1SD
% > B532+2SD
F532 % Sat.
F3 Median
F3 Mean
F3 SD
B3 Median
B3 Mean
B3 SD
% > B3+1SD
% > B3+2SD
F3 % Sat.
F4 Median
F4 Mean
F4 SD
B4 Median
B4 Mean
B4 SD
% > B4+1SD
% > B4+2SD
F4 % Sat.
Ratio of Medians (635/532)
Ratio of Means (635/532)
Median of Ratios (635/532)
Mean of Ratios (635/532)
Ratios SD (635/532)
Rgn Ratio (635/532)
Rgn R2 (635/532)
Ratio of Medians (Ratio/2)
Ratio of Means (Ratio/2)
Median of Ratios (Ratio/2)
Mean of Ratios (Ratio/2)
Ratios SD (Ratio/2)
Rgn Ratio (Ratio/2)
Rgn R2 (Ratio/2)
Ratio of Medians (Ratio/3)
Ratio of Means (Ratio/3)
Median of Ratios (Ratio/3)
Mean of Ratios (Ratio/3)
Ratios SD (Ratio/3)
Rgn Ratio (Ratio/3)
Rgn R2 (Ratio/3)
F Pixels
B Pixels
Sum of Medians
Sum of Means
Log Ratio (635/532)
Log Ratio (Ratio/2)
Log Ratio (Ratio/3)
F635 Median - B635
F532 Median - B532
F3 Median - B3
F4 Median - B4
F635 Mean - B635
F532 Mean - B532
F3 Mean - B3
F4 Mean - B4
Flags
Normalize
UNF_VALUE Log Ratio (635/532)
INV_VALUE Log Ratio (635/532) with flagged values removed

Data table
ID_REF VALUE F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. F3 Median F3 Mean F3 SD B3 Median B3 Mean B3 SD % > B3+1SD % > B3+2SD F3 % Sat. F4 Median F4 Mean F4 SD B4 Median B4 Mean B4 SD % > B4+1SD % > B4+2SD F4 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) Ratio of Medians (Ratio/2) Ratio of Means (Ratio/2) Median of Ratios (Ratio/2) Mean of Ratios (Ratio/2) Ratios SD (Ratio/2) Rgn Ratio (Ratio/2) Rgn R2 (Ratio/2) Ratio of Medians (Ratio/3) Ratio of Means (Ratio/3) Median of Ratios (Ratio/3) Mean of Ratios (Ratio/3) Ratios SD (Ratio/3) Rgn Ratio (Ratio/3) Rgn R2 (Ratio/3) F Pixels B Pixels Sum of Medians Sum of Means Log Ratio (635/532) Log Ratio (Ratio/2) Log Ratio (Ratio/3) F635 Median - B635 F532 Median - B532 F3 Median - B3 F4 Median - B4 F635 Mean - B635 F532 Mean - B532 F3 Mean - B3 F4 Mean - B4 Flags Normalize UNF_VALUE INV_VALUE
1 -0.111 24075 30240 15500 165 205 145 100 100 7 22248 27593 16107 99 199 237 100 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.08 1.094 1.049 1.204 1.839 1.025 0.797 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 965 46323 57833 0.111 Error Error 24075 22248 0 0 30240 27593 0 0 0 0 0.111 0.111
2 -0.017 24886 31863 15226 179 224 174 100 100 5 24524 30532 14932 107 230 282 100 100 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.012 1.041 0.998 1.058 1.412 1.054 0.835 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 786 49410 62395 0.017 Error Error 24886 24524 0 0 31863 30532 0 0 0 0 0.017 0.017
3 -0.031 24001 31491 16490 175 223 170 100 100 7 23411 29518 15317 107 227 252 100 100 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.022 1.065 1.009 1.062 1.338 1.074 0.897 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 786 47412 61009 0.031 Error Error 24001 23411 0 0 31491 29518 0 0 0 0 0.031 0.031
4 -0.098 9596 12557 7496 170 213 149 100 100 0 8913 12143 8069 101 198 214 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.07 1.029 1.075 1.039 1.355 0.964 0.875 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 804 18509 24700 0.098 Error Error 9596 8913 0 0 12557 12143 0 0 0 0 0.098 0.098
5 -0.072 10738 13158 6768 172 205 124 100 100 0 10158 12548 7808 102 197 201 100 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.051 1.043 1.069 1.109 1.472 0.939 0.834 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 790 20896 25706 0.072 Error Error 10738 10158 0 0 13158 12548 0 0 0 0 0.072 0.072
6 -0.064 10316 13171 7146 168 200 122 100 100 0 9810 12297 7181 103 204 212 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.045 1.066 1.096 1.091 1.407 0.977 0.836 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 775 20126 25468 0.064 Error Error 10316 9810 0 0 13171 12297 0 0 0 0 0.064 0.064
7 -0.044 25949 28600 12076 170 221 338 100 100 0 25096 27367 11307 104 217 329 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.031 1.043 1.033 1.04 1.217 1.007 0.908 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 845 51045 55967 0.044 Error Error 25949 25096 0 0 28600 27367 0 0 0 0 0.044 0.044
8 -0.132 33565 35171 10178 167 213 150 100 100 0 30566 31944 10149 104 216 246 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.096 1.099 1.095 1.108 1.233 1.046 0.896 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 856 64131 67115 0.132 Error Error 33565 30566 0 0 35171 31944 0 0 0 0 0.132 0.132
9 -0.138 32098 34039 11156 168 210 149 100 100 0 29147 31127 10663 114 233 268 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.1 1.092 1.084 1.098 1.236 1.045 0.88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 777 61245 65166 0.138 Error Error 32098 29147 0 0 34039 31127 0 0 0 0 0.138 0.138
10 0.103 3533 4318 2747 166 200 129 100 100 0 3725 4560 3424 108 217 238 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.931 0.933 0.955 0.983 1.635 0.865 0.604 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 868 7258 8878 -0.103 Error Error 3533 3725 0 0 4318 4560 0 0 0 0 -0.103 -0.103
11 -0.01 3808 4451 2518 149 184 111 100 100 0 3737 4639 3487 102 203 210 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.007 0.948 0.978 0.999 1.756 0.872 0.596 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 879 7545 9090 0.01 Error Error 3808 3737 0 0 4451 4639 0 0 0 0 0.01 0.01
12 -0.047 3500 4267 2792 141 181 119 100 100 0 3354 4161 3597 103 209 251 98 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.033 1.017 1.024 1.164 2.246 0.964 0.414 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 870 6854 8428 0.047 Error Error 3500 3354 0 0 4267 4161 0 0 0 0 0.047 0.047
13 -0.595 8322 9865 4652 149 190 127 100 100 0 5517 6572 3582 104 215 267 100 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.51 1.502 1.451 1.593 1.753 1.428 0.535 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 1007 13839 16437 0.595 Error Error 8322 5517 0 0 9865 6572 0 0 0 0 0.595 0.595
14 -0.621 9319 11365 5393 159 205 136 100 100 0 6065 7097 3941 111 237 526 98 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.538 1.604 1.522 1.729 2.119 1.607 0.487 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 945 15384 18462 0.621 Error Error 9319 6065 0 0 11365 7097 0 0 0 0 0.621 0.621
15 -0.561 8503 10227 4813 149 196 161 100 100 0 5761 6677 4466 99 214 425 96 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.475 1.532 1.606 1.798 2.149 1.479 0.629 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 882 14264 16904 0.561 Error Error 8503 5761 0 0 10227 6677 0 0 0 0 0.561 0.561
16 217 249 137 148 188 151 29 7 0 137 261 273 100 214 408 14 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.865 0.627 1.009 0.973 6.965 0.16 0.023 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 962 354 510 0.899 Error Error 217 137 0 0 249 261 0 0 -50 0 0.899
17 -0.792 264 299 133 167 202 121 42 25 0 157 263 215 101 186 171 36 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.732 0.815 0.521 0.824 7.28 0.058 0.003 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 372 421 562 0.792 Error Error 264 157 0 0 299 263 0 0 0 0 0.792 0.792
18 216 243 144 157 194 123 29 9 0 177 284 262 102 190 178 33 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.787 0.473 1.148 1.021 5.995 0.034 0.001 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 1104 393 527 -0.346 Error Error 216 177 0 0 243 284 0 0 -50 0 -0.346
19 163 195 112 167 203 145 16 1 0 101 194 171 101 209 246 17 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100000 0.301 2.617 1.843 5.182 0.188 0.058 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 883 264 389 16.61 Error Error 163 101 0 0 195 194 0 0 -50 0 16.61
20 160 198 124 179 220 166 14 3 0 119 225 203 107 237 275 20 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1.583 0.161 2.868 1.806 5.405 0.105 0.019 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 752 279 423 Error Error Error 160 119 0 0 198 225 0 0 -50 0

Total number of rows: 11520

Table truncated, full table size 3022 Kbytes.




Supplementary file Size Download File type/resource
GSM200010.gpr.gz 917.1 Kb (ftp)(http) GPR
Processed data included within Sample table
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