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Sample GSM98971 Query DataSets for GSM98971
Status Public on Sep 01, 2006
Title Rat neonatal cardiomyocytes, prorenin-Cy5 vs control-Cy3, slide_07
Sample type RNA
 
Channel 1
Source name Rat neonatal cardiomyocytes, prorenin-Cy5
Organism Rattus norvegicus
Characteristics Rat neonatal cardiomyocytes, vehicle 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 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, control-Cy3
Organism Rattus norvegicus
Characteristics Rat neonatal cardiomyocytes, prorenin (2 nM) 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 Mar 05, 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
1 100 3267 2866 1000 135 147 61 100 100 0 4011 3609 1321 103 124 83 100 100 0 0.801 0.779 0.785 0.773 1.334 0.773 0.968 80 560 7040 6237 -0.319 3132 3908 2731 3506 0 -0.319
2 100 1910 1609 646 153 164 44 96 96 0 2230 1886 726 110 118 42 98 98 0 0.829 0.82 0.816 0.758 1.538 0.835 0.959 80 560 3877 3232 -0.271 1757 2120 1456 1776 0 -0.271
3 100 8630 7157 4209 179 513 1463 80 73 0 7805 6528 3269 143 285 508 90 86 0 1.103 1.093 1.086 0.962 1.7 1.175 0.925 80 560 16113 13363 0.141 8451 7662 6978 6385 -50 null
4 80 360 399 137 133 135 16 100 100 0 788 764 204 85 88 14 100 100 0 0.323 0.392 0.328 0.369 1.555 0.447 0.659 52 340 930 945 -1.631 227 703 266 679 0 -1.631
5 90 535 525 81 141 145 26 100 100 0 937 923 163 98 103 24 100 100 0 0.47 0.465 0.46 0.464 1.205 0.447 0.93 52 420 1233 1209 -1.09 394 839 384 825 0 -1.09
6 100 593 562 211 133 135 19 100 100 0 662 631 277 76 79 17 100 100 0 0.785 0.773 0.763 0.79 1.321 0.767 0.955 80 560 1046 984 -0.349 460 586 429 555 0 -0.349
7 90 279 291 57 137 139 27 100 98 0 259 265 47 89 91 21 100 100 0 0.835 0.875 0.861 0.84 1.376 0.93 0.732 52 420 312 330 -0.26 142 170 154 176 0 -0.26
8 90 195 204 30 126 127 13 100 100 0 245 248 41 80 82 18 100 100 0 0.418 0.464 0.462 0.451 1.351 0.486 0.658 52 420 234 246 -1.258 69 165 78 168 0 -1.258
9 90 175 206 148 132 134 16 92 71 0 160 176 53 87 90 19 100 100 0 0.589 0.831 0.597 0.548 1.897 1.911 0.549 52 420 116 163 -0.764 43 73 74 89 0 -0.764
10 100 626 633 284 139 151 44 93 91 0 503 494 205 99 124 60 90 88 0 1.205 1.251 1.301 1.23 1.534 1.303 0.914 80 560 891 889 0.27 487 404 494 395 -50 null
11 80 771 787 104 133 135 22 100 100 0 588 585 58 90 92 13 100 100 0 1.281 1.321 1.343 1.314 1.16 1.355 0.938 52 340 1136 1149 0.357 638 498 654 495 0 0.357
12 80 746 747 138 135 145 62 100 100 0 540 522 61 78 85 38 100 100 0 1.323 1.378 1.375 1.357 1.223 1.445 0.932 52 340 1073 1056 0.403 611 462 612 444 0 0.403
13 90 175 178 22 138 142 27 71 19 0 138 138 13 91 93 14 100 92 0 0.787 0.851 0.813 0.757 1.81 1.577 0.363 52 420 84 87 -0.345 37 47 40 47 0 -0.345
14 100 162 175 43 135 188 127 5 0 0 162 186 65 107 195 190 8 0 0 0.491 0.506 0.475 0.49 2.051 0.55 0.907 80 560 82 119 -1.026 27 55 40 79 -50 null
15 100 149 150 21 135 145 61 2 0 0 105 108 28 82 86 27 37 8 0 0.609 0.577 0.698 0.76 2.564 2.305 0.112 80 560 37 41 -0.716 14 23 15 26 -50 null
16 90 1268 1282 110 164 173 46 100 100 0 900 885 125 129 135 32 100 100 0 1.432 1.479 1.435 1.497 1.184 1.466 0.941 52 420 1875 1874 0.518 1104 771 1118 756 0 0.518
17 100 852 794 290 135 158 73 90 87 0 799 745 289 98 202 246 86 81 0 1.023 1.019 1.03 0.942 1.648 1.015 0.88 80 560 1418 1306 0.033 717 701 659 647 -50 null
18 100 982 992 221 128 263 1858 0 0 0 794 799 201 79 132 606 81 2 0 1.194 1.2 1.19 1.202 1.299 1.209 0.941 80 560 1569 1584 0.256 854 715 864 720 0 0.256
19 130 597 775 494 153 165 69 100 96 0 783 922 538 122 149 138 100 79 0 0.672 0.777 0.719 0.729 1.37 0.869 0.875 120 846 1105 1422 -0.574 444 661 622 800 0 -0.574
20 100 1132 5253 9204 382 826 2003 30 25 0 1057 4380 6514 318 785 1800 33 26 0 1.015 1.199 0.932 0.989 1.427 1.298 0.887 80 560 1489 8933 0.021 750 739 4871 4062 -50 null

Total number of rows: 16416

Table truncated, full table size 2529 Kbytes.




Supplementary data files not provided
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