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Sample GSM98589 Query DataSets for GSM98589
Status Public on Sep 01, 2006
Title Rat neonatal cardiomyocytes, Ang-Cy5 vs control-Cy3, slide_04
Sample type RNA
 
Channel 1
Source name Rat neonatal cardiomyocytes, AngII-Cy5
Organism Rattus norvegicus
Characteristics Rat neonatal cardiomyocytes, Angiotensin-II stimulated for 4 hours
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. RNA of 5 independent preparations was equimolar pooled and lineair amplified.
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, vehicle incubated for 4 hours
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. RNA of 5 independent preparations was equimolar pooled and lineair amplified.
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 90 1739 1586 607 145 149 38 100 100 0 4517 4047 1389 88 94 66 100 100 0 0.36 0.364 0.356 0.358 1.356 0.392 0.914 52 420 6023 5400 -1.474 1594 4429 1441 3959 0 -1.474
2 100 2101 1967 1136 150 151 14 100 100 0 4806 4113 1690 102 103 11 100 100 0 0.415 0.453 0.415 0.464 1.495 0.465 0.779 80 560 6655 5828 -1.27 1951 4704 1817 4011 0 -1.27
3 90 2475 2201 765 162 163 19 100 100 0 5551 4677 1763 119 124 30 100 100 0 0.426 0.447 0.439 0.445 1.403 0.433 0.921 52 420 7745 6597 -1.232 2313 5432 2039 4558 0 -1.232
4 90 746 742 80 176 177 16 100 100 0 1329 1259 175 134 136 17 100 100 0 0.477 0.503 0.507 0.505 1.147 0.493 0.964 52 420 1765 1691 -1.068 570 1195 566 1125 0 -1.068
5 80 1090 1045 264 175 175 16 100 100 0 1272 1192 290 121 121 11 100 100 0 0.795 0.812 0.819 0.805 1.208 0.82 0.965 52 340 2066 1941 -0.331 915 1151 870 1071 0 -0.331
6 80 651 681 373 171 172 14 100 100 0 930 895 258 122 122 11 100 100 0 0.594 0.66 0.578 0.615 1.412 0.771 0.671 52 340 1288 1283 -0.751 480 808 510 773 0 -0.751
7 100 275 289 61 191 192 28 95 78 0 246 248 55 144 145 18 98 90 0 0.824 0.942 0.898 0.896 2.003 1 0.747 80 544 186 202 -0.28 84 102 98 104 0 -0.28
8 80 223 226 21 181 183 19 88 61 0 190 187 26 132 134 13 92 88 0 0.724 0.818 0.758 0.762 2.297 0.859 0.355 52 340 100 100 -0.466 42 58 45 55 0 -0.466
9 80 276 276 26 210 211 22 94 84 0 275 278 29 175 177 17 100 98 0 0.66 0.641 0.671 0.612 1.566 0.633 0.575 52 340 166 169 -0.599 66 100 66 103 0 -0.599
10 80 379 380 57 152 153 14 100 100 0 421 415 79 96 97 10 100 100 0 0.698 0.715 0.713 0.714 1.202 0.703 0.929 52 340 552 547 -0.518 227 325 228 319 0 -0.518
11 80 371 367 54 159 159 15 100 100 0 438 422 56 105 105 10 100 100 0 0.637 0.656 0.66 0.636 1.262 0.652 0.905 52 340 545 525 -0.651 212 333 208 317 0 -0.651
12 90 337 347 35 155 157 14 100 100 0 416 422 29 101 101 10 100 100 0 0.578 0.598 0.596 0.593 1.192 0.596 0.909 52 420 497 513 -0.791 182 315 192 321 0 -0.791
13 70 195 192 17 155 156 14 90 68 0 172 178 28 114 114 12 100 100 0 0.69 0.578 0.649 0.587 1.784 0.584 0.399 32 236 98 101 -0.536 40 58 37 64 0 -0.536
14 70 730 2676 6371 240 425 965 25 15 0 1059 1514 1312 247 340 336 75 59 0 0.603 1.923 0.73 0.84 2.407 4.155 0.67 32 230 1302 3703 -0.729 490 812 2436 1267 -100 null
15 90 204 202 20 157 157 15 96 78 0 152 151 15 99 100 10 100 100 0 0.887 0.865 0.915 0.84 1.689 0.995 0.446 52 420 100 97 -0.173 47 53 45 52 0 -0.173
16 100 424 423 71 224 227 23 100 96 0 388 390 89 176 177 15 100 97 0 0.943 0.93 0.927 0.974 1.647 0.884 0.772 80 540 412 413 -0.084 200 212 199 214 0 -0.084
17 90 701 688 81 159 161 25 100 100 0 710 699 70 107 112 43 100 100 0 0.899 0.894 0.896 0.89 1.178 0.882 0.955 52 420 1145 1121 -0.154 542 603 529 592 0 -0.154
18 100 734 693 141 169 170 18 100 100 0 798 727 178 128 130 25 98 98 0 0.843 0.875 0.855 0.915 1.441 0.864 0.945 80 560 1235 1123 -0.246 565 670 524 599 0 -0.246
19 120 358 371 101 156 238 456 3 0 0 409 411 105 112 184 309 42 1 0 0.68 0.719 0.677 0.698 1.464 1.378 0.706 120 771 499 514 -0.556 202 297 215 299 0 -0.556
20 120 240 258 129 166 173 41 90 32 0 267 275 63 145 158 46 99 86 0 0.607 0.708 0.607 0.612 1.478 1.215 0.638 120 747 196 222 -0.721 74 122 92 130 0 -0.721

Total number of rows: 16416

Table truncated, full table size 2520 Kbytes.




Supplementary data files not provided
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