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Sample GSM97745 Query DataSets for GSM97745
Status Public on Sep 01, 2006
Title Rat neonatal cardiomyocytes, control-Cy5 vs prorenin-Cy3, slide-6
Sample type RNA
 
Channel 1
Source name Rat neonatal cardiomyocytes, control-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 Prepared neonatal rat purified cardiomyocytes were step-wise serum deprived, 4 days, day 5 in DMEM/199 (4:1) plus 1% BSA. Cells were plated in 9.6 cm2 dishes in high density (1,500,000 cells/dish). After stimulation for 4 hours, cells were harvested by chilling on ice, 3x rinsing with cold PBS, followed by pelleting of the cells.
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, prorenin-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 Prepared neonatal rat purified cardiomyocytes were step-wise serum deprived, 4 days, day 5 in DMEM/199 (4:1) plus 1% BSA. Cells were plated in 9.6 cm2 dishes in high density (1,500,000 cells/dish). After stimulation for 4 hours, cells were harvested by chilling on ice, 3x rinsing with cold PBS, followed by pelleting of the cells.
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 21, 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 1208 1046 370 221 225 44 93 91 0 2209 1973 858 105 115 108 95 91 0 0.469 0.442 0.428 0.421 1,596 0.435 0.957 80 560 3091 2693 -1092 987 2104 825 1868 0 -1092
2 90 827 828 83 217 219 23 100 100 0 1558 1544 179 119 121 16 100 100 0 0.424 0.429 0.433 0.429 1,108 0.427 0.96 52 420 2049 2036 -1238 610 1439 611 1425 0 -1238
3 100 1283 1311 621 213 268 311 85 80 0 4241 3937 1879 121 192 253 93 93 0 0.26 0.288 0.273 0.268 1,546 0.293 0.892 80 560 5190 4914 -1945 1070 4120 1098 3816 0 -1945
4 90 1151 1082 237 255 263 42 100 100 0 1204 1156 210 137 149 47 100 100 0 0.84 0.812 0.83 0.779 1,262 0.833 0.962 52 420 1963 1846 -0.252 896 1067 827 1019 0 -0.252
5 70 768 943 749 234 245 56 100 100 0 865 900 463 122 140 80 100 100 0 0.719 0.911 0.738 0.811 1.41 1,199 0.586 32 236 1277 1487 -0.477 534 743 709 778 0 -0.477
6 90 521 512 102 195 198 36 100 100 0 607 597 143 112 113 16 100 100 0 0.659 0.654 0.66 0.647 1,188 0.655 0.944 52 420 821 802 -0.603 326 495 317 485 0 -0.603
7 100 296 297 28 290 290 23 28 8 0 142 144 22 123 124 11 62 43 0 0.316 0.333 0.964 0.882 3,856 2,886 0.089 80 560 25 28 -1663 6 19 7 21 -50
8 60 246 244 23 194 196 21 93 65 0 138 143 17 96 96 10 100 96 0 1,238 1,064 1,051 1,006 1,741 1313 0.453 32 176 94 97 0.308 52 42 50 47 0 0.308
9 120 263 275 80 200 203 27 79 56 0 230 265 119 110 113 19 97 97 0 0.525 0.484 0.436 0.404 2,042 0.55 0.689 120 797 183 230 -0.93 63 120 75 155 0 -0.93
10 90 367 370 39 212 214 25 100 100 0 431 422 48 103 107 19 100 100 0 0.473 0.495 0.469 0.488 1,292 0.503 0.816 52 420 483 477 -1,081 155 328 158 319 0 -1081
11 90 385 379 38 220 221 20 100 100 0 435 427 53 110 110 11 100 100 0 0.508 0.502 0.495 0.494 1,265 0.5 0.871 52 420 490 476 -0.978 165 325 159 317 0 -0.978
12 80 341 339 37 200 206 49 100 86 0 430 423 39 110 116 54 100 100 0 0.441 0.444 0.435 0.433 1,296 0.545 0.803 52 340 461 452 -1,182 141 320 139 313 0 -1182
13 100 211 215 22 196 198 20 41 16 0 105 104 11 97 98 12 31 6 0 1,875 2714 1,906 1,794 3,688 3,844 0.151 80 560 23 26 0.907 15 8 19 7 -50
14 50 281 294 35 226 229 21 100 75 0 152 155 17 116 118 16 91 66 0 1528 1744 1,892 1,727 1,483 1,773 0.613 12 104 91 107 0.611 55 36 68 39 0 0.611
15 100 210 211 26 200 202 25 28 6 0 114 116 17 106 109 16 30 7 0 1.25 1.1 1,694 1,449 2,588 2,246 0.314 80 560 18 21 0.322 10 8 11 10 -50
16 100 630 610 88 192 193 23 100 100 0 755 691 153 97 99 16 100 100 0 0.666 0.704 0.692 0.721 1,236 0.691 0.96 80 560 1096 1012 -0.587 438 658 418 594 0 -0.587
17 100 574 566 97 215 214 20 100 98 0 651 632 108 109 110 11 100 100 0 0.662 0.671 0.674 0.648 1.37 0.693 0.941 80 560 901 874 -0.594 359 542 351 523 0 -0.594
18 100 475 458 69 206 208 29 100 98 0 518 499 76 111 113 22 100 100 0 0.661 0.649 0.646 0.628 1,268 0.671 0.908 80 560 676 640 -0.597 269 407 252 388 0 -0.597
19 110 466 465 62 346 397 289 2 0 0 408 402 63 196 254 269 12 0 0 0.566 0.578 0.571 0.531 1,536 1171 0.497 80 652 332 325 -0.821 120 212 119 206 0 -0.821
20 100 346 354 60 315 417 411 1 0 0 297 298 34 256 365 380 0 0 0 0.756 0.929 1015 0.929 2,157 1809 0.899 80 560 72 81 -0.403 31 41 39 42 -50

Total number of rows: 16416

Table truncated, full table size 2431 Kbytes.




Supplementary data files not provided
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