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Sample GSM98588 Query DataSets for GSM98588
Status Public on Sep 01, 2006
Title Rat neonatal cardiomyocytes, Prorenin-Cy5 vs Ang-Cy3, slide_05
Sample type RNA
 
Channel 1
Source name Rat neonatal cardiomyocytes, prorenin-Cy5
Organism Rattus norvegicus
Characteristics Rat neonatal cardiomyocytes, prorenin (2 nM) stimulated for 4 hours. Total RNA of 5 independent preparations was equimolar pooled and lineair amplified.
Growth protocol Neonatal rat cardiomyocytes, step-wise serum deprived in 4 days, day 5 in DMEM/199 (4:1) plus 1% BSA, plated in high density (1,500,000 cells/dish). After stimulation for 4 hours, cells were chilled, 3x rinsed with cold PBS, and pelleted.
Extracted molecule total RNA
Extraction protocol RNA isolation was accomplished with Sigma-Aldrich Tri-reagent and verified using lab-on-chip and UV-spectrum analysis.
Label Cy5
Label protocol The cRNA from prorenin stimulated and control cells was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit.
 
Channel 2
Source name Rat neonatal cardiomyocytes, AngII-Cy3
Organism Rattus norvegicus
Characteristics Rat neonatal cardiomyocytes, AngII (100nM) incubated for 4 hours. Total RNA of 5 independent preparations was equimolar pooled and lineair amplified.
Growth protocol Neonatal rat cardiomyocytes, step-wise serum deprived in 4 days, day 5 in DMEM/199 (4:1) plus 1% BSA, plated in high density (1,500,000 cells/dish). After stimulation for 4 hours, cells were chilled, 3x rinsed with cold PBS, and pelleted.
Extracted molecule total RNA
Extraction protocol RNA isolation was accomplished with Sigma-Aldrich Tri-reagent and verified using lab-on-chip and UV-spectrum analysis.
Label Cy3
Label protocol The cRNA from prorenin stimulated and control cells was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit.
 
 
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a Agilent G2505A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software.
Description high density plated, purified, serum-deprived purified Wistar Rat neonatal cardiomyocytes
Data processing After background correction and removal of flagged values, log base 2 expression ratios were derived
 
Submission date Feb 27, 2006
Last update date Apr 18, 2023
Contact name Jasper Saris
Organization name Erasmus Medical Center
Street address Dr. Molewaterplein 50
City Rotterdam
State/province Zuid holland
ZIP/Postal code 3015GE
Country Netherlands
 
Platform ID GPL3410
Series (1)
GSE4340 Establishing a functional response of cardiomyocytes upon prorenin stimulation.

Data table header descriptions
ID_REF
Dia. Diameter of the spot
F635 Median Intensity Channel 1, F635 Median
F635 Mean Mean signal intensity Channel 1
F635 SD Standard deviation intensity Channel 1
B635 Median Median background of Channel 1
B635 Mean Mean background of Channel 1
B635 SD standard deviation of Channel 1 background
% > B635+1SD Percentage of pixels that have a higher intensity than the Channel 1 background plus 1 SD
% > B635+2SD Percentage of pixels that is higher than the Channel 1 backgound plus 2 SD
F635 % Sat. Percentage saturated pixels Channel 1
F532 Median Intensity Channel 2, F532 Median
F532 Mean Mean signal intensity Channel 2
F532 SD Standard deviation intensity Channel 2
B532 Median Median background of Channel 2
B532 Mean Mean background of Channel 2
B532 SD standard deviation of Channel 2 background
% > B532+1SD Percentage of pixels that have a higher intensity than the Channel 2 background plus 1 SD
% > B532+2SD Percentage of pixels that is higher than the Channel 2 backgound plus 2 SD
F532 % Sat. Percentage saturated pixels Channel 2
Ratio of Medians Ratio of median intensities
Ratio of Means Ratio of mean intensities
Median of Ratios Median of ratios
Mean of Ratios Mean of ratios
Ratios SD Standard deviation
Rgn Ratio Regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn R� Coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F Pixels Number of pixels in the foreground
B Pixels Number of pixels in the background
Sum of Medians Sum of medians
Sum of Means Sum of means
Log Ratio Log ratio
F635 Median - B635 Median intensity of channel 1 minus the local background
F532 Median - B532 Median intensity of channel 2 minus the local background
F635 Mean - B635 Median intensity of target minus the local background
F532 Mean - B532 Median intensity of the reference sample minus the local background
Flags Negative number means the spot is bad or not found
VALUE normalized log10 ratio of channel 1 divided by channel two (ratio profiles, Rosetta Resolver)

Data table
ID_REF Dia. 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. Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R� F Pixels B Pixels Sum of Medians Sum of Means Log Ratio F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags VALUE
1 110 1881 1812 344 177 180 29 100 100 0 3388 3206 594 127 135 54 100 100 0 0.523 0.531 0.525 0.528 1.137 0.532 0.967 80 650 4965 4714 -0.936 1704 3261 1635 3079 0 -0.936
2 120 2846 4005 3968 203 225 80 98 91 0 5694 5378 3166 168 200 101 100 97 0 0.478 0.73 0.579 0.589 1.792 0.929 0.75 120 776 8169 9012 -1.064 2643 5526 3802 5210 0 -1.064
3 100 3509 3216 1183 193 195 17 100 100 0 6355 5679 2309 145 146 15 100 100 0 0.534 0.546 0.531 0.553 1.25 0.536 0.973 80 560 9526 8557 -0.905 3316 6210 3023 5534 0 -0.905
4 100 833 786 180 190 202 77 97 96 0 1256 1180 248 120 137 75 98 98 0 0.566 0.562 0.563 0.546 1.232 0.571 0.953 80 560 1779 1656 -0.821 643 1136 596 1060 0 -0.821
5 100 876 1026 739 180 202 165 96 90 0 1640 1623 505 115 149 225 98 98 0 0.456 0.561 0.47 0.48 1.481 0.705 0.694 80 560 2221 2354 -1.132 696 1525 846 1508 0 -1.132
6 100 996 928 221 215 249 90 97 95 0 1600 1487 453 154 240 185 97 93 0 0.54 0.535 0.538 0.545 1.215 0.518 0.944 80 536 2227 2046 -0.889 781 1446 713 1333 -50 null
7 100 288 319 133 278 308 241 6 2 0 178 193 70 148 173 124 6 2 0 0.333 0.911 0.911 0.963 3.384 1.584 0.43 80 560 40 86 -1.585 10 30 41 45 -50 null
8 110 237 242 32 183 187 61 37 3 0 193 200 39 109 114 26 100 87 0 0.643 0.648 0.654 0.599 1.794 0.722 0.577 80 650 138 150 -0.637 54 84 59 91 0 -0.637
9 120 292 294 32 219 220 19 98 85 0 223 225 33 140 141 13 98 96 0 0.88 0.882 0.917 0.883 1.842 0.918 0.658 120 772 156 160 -0.185 73 83 75 85 0 -0.185
10 100 1221 1295 405 545 617 300 92 58 0 1418 1528 457 797 903 536 55 25 0 1.089 1.026 1.052 1.1 1.432 0.764 0.798 80 560 1297 1481 0.122 676 621 750 731 -50 null
11 100 401 398 46 184 186 20 100 100 0 456 445 46 118 120 14 100 100 0 0.642 0.654 0.659 0.646 1.2 0.664 0.898 80 555 555 541 -0.639 217 338 214 327 0 -0.639
12 100 434 432 69 201 207 33 100 98 0 520 504 86 153 155 19 100 100 0 0.635 0.658 0.656 0.65 1.201 0.671 0.893 80 560 600 582 -0.655 233 367 231 351 0 -0.655
13 100 226 226 20 212 214 24 32 5 0 158 157 16 134 136 12 76 43 0 0.583 0.609 0.684 0.686 2.816 4.065 0.023 80 560 38 37 -0.778 14 24 14 23 -50 null
14 60 244 245 19 206 207 27 68 15 0 169 169 21 131 136 23 75 37 0 1 1.026 0.895 0.952 2.427 1.394 0.202 32 176 76 77 0 38 38 39 38 0 0
15 100 240 240 22 212 215 25 56 13 0 197 198 30 152 152 12 86 77 0 0.622 0.609 0.609 0.593 3.098 0.747 0.047 80 560 73 74 -0.684 28 45 28 46 -50 null
16 120 537 559 145 290 294 45 100 99 0 451 455 111 147 149 22 100 98 0 0.813 0.873 0.823 0.857 1.35 0.958 0.809 120 775 551 577 -0.3 247 304 269 308 0 -0.3
17 120 497 494 56 176 177 15 100 100 0 576 556 82 114 114 10 100 100 0 0.695 0.719 0.708 0.728 1.209 0.705 0.958 120 771 783 760 -0.525 321 462 318 442 0 -0.525
18 120 636 622 97 229 230 22 99 99 0 637 631 76 152 154 18 100 100 0 0.839 0.82 0.842 0.797 1.31 0.844 0.947 120 774 892 872 -0.253 407 485 393 479 0 -0.253
19 100 285 359 213 233 275 156 21 8 0 278 372 352 188 259 223 16 7 0 0.578 0.685 0.667 0.553 2.65 0.773 0.726 80 560 142 310 -0.791 52 90 126 184 -50 null
20 100 357 358 40 298 299 57 51 11 0 543 548 44 434 433 114 43 2 0 0.541 0.526 0.548 0.526 2.345 0.667 0.691 80 560 168 174 -0.886 59 109 60 114 -50 null

Total number of rows: 16416

Table truncated, full table size 2537 Kbytes.




Supplementary data files not provided
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