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Sample GSM98972 Query DataSets for GSM98972
Status Public on Aug 31, 2006
Title Rat neonatal cardiomyocytes, AngII-Cy5 vs control-Cy3, slide_09, dye-swap
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 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 (100 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 6782 6567 1393 167 168 21 100 100 0 4816 4553 1278 100 102 17 100 100 0 1.403 1.437 1.417 1.5 1.288 1.407 0.968 80 560 11331 10853 0.488 6615 4716 6400 4453 0 0.488
2 100 7765 7223 2276 199 201 20 100 100 0 5523 4969 1818 95 97 15 100 100 0 1.394 1.441 1.411 1.553 1.307 1.411 0.972 80 560 12994 11898 0.479 7566 5428 7024 4874 0 0.479
3 90 8586 8385 773 163 163 15 100 100 0 7318 7091 775 108 110 17 100 100 0 1.168 1.177 1.171 1.18 1.105 1.165 0.969 52 420 15633 15205 0.224 8423 7210 8222 6983 0 0.224
4 80 781 828 250 160 160 16 100 100 0 863 822 175 106 109 18 100 100 0 0.82 0.933 0.866 0.901 1.239 0.997 0.932 52 340 1378 1384 -0.286 621 757 668 716 0 -0.286
5 80 833 834 334 156 157 14 100 100 0 669 673 216 95 98 14 100 100 0 1.179 1.173 1.083 1.087 1.346 1.259 0.937 52 340 1251 1256 0.238 677 574 678 578 0 0.238
6 100 359 412 159 162 177 79 95 68 0 335 368 142 104 123 122 95 41 0 0.853 0.947 0.885 0.905 1.264 0.797 0.826 80 560 428 514 -0.23 197 231 250 264 0 -0.23
7 80 251 253 28 168 181 80 51 1 0 243 245 28 122 127 33 100 98 0 0.686 0.691 0.708 0.675 1.458 0.931 0.37 52 340 204 208 -0.544 83 121 85 123 0 -0.544
8 80 212 208 23 147 150 21 94 78 0 196 200 33 94 100 27 100 100 0 0.637 0.575 0.619 0.548 1.454 0.61 0.723 52 340 167 167 -0.65 65 102 61 106 0 -0.65
9 70 203 204 22 150 153 20 96 71 0 167 167 18 84 96 33 100 90 0 0.639 0.651 0.654 0.596 1.71 0.694 0.641 32 236 136 137 -0.647 53 83 54 83 0 -0.647
10 90 715 703 72 175 176 15 100 100 0 591 581 59 100 102 13 100 100 0 1.1 1.098 1.1 1.096 1.12 1.105 0.96 52 420 1031 1009 0.137 540 491 528 481 0 0.137
11 90 723 720 88 146 147 15 100 100 0 631 613 63 93 95 15 100 100 0 1.072 1.104 1.112 1.099 1.141 1.12 0.957 52 420 1115 1094 0.101 577 538 574 520 0 0.101
12 80 763 762 101 157 157 15 100 100 0 677 646 118 95 96 11 100 100 0 1.041 1.098 1.114 1.117 1.165 1.085 0.952 52 340 1188 1156 0.058 606 582 605 551 0 0.058
13 100 222 223 23 202 204 25 40 11 0 149 147 34 104 107 20 72 57 0 0.444 0.488 0.535 0.541 2.73 0.937 0.218 80 560 65 64 -1.17 20 45 21 43 -50 null
14 80 175 178 25 149 149 14 67 46 0 137 136 19 91 91 12 94 86 0 0.565 0.644 0.682 0.648 2.368 0.746 0.307 52 340 72 74 -0.823 26 46 29 45 0 -0.823
15 70 187 188 17 151 152 15 93 62 0 148 147 16 94 96 12 96 96 0 0.667 0.698 0.696 0.679 1.814 0.844 0.397 32 236 90 90 -0.585 36 54 37 53 0 -0.585
16 100 1266 1195 245 171 172 20 100 100 0 1216 1127 242 95 96 11 100 100 0 0.977 0.992 0.978 0.985 1.275 0.994 0.959 80 560 2216 2056 -0.034 1095 1121 1024 1032 0 -0.034
17 110 1288 1248 485 149 180 696 88 6 0 1063 978 320 89 89 12 100 98 0 1.169 1.236 1.162 1.323 1.538 263.523 0.002 80 650 2113 1988 0.226 1139 974 1099 889 0 0.226
18 100 1417 1344 258 148 149 14 100 100 0 1209 1130 228 79 80 12 100 100 0 1.123 1.138 1.138 1.13 1.339 1.142 0.961 80 560 2399 2247 0.167 1269 1130 1196 1051 0 0.167
19 160 490 471 92 191 194 32 98 95 0 333 322 64 106 108 32 97 95 0 1.317 1.296 1.29 1.272 1.543 1.338 0.911 208 1130 526 496 0.397 299 227 280 216 0 0.397
20 130 343 355 60 211 218 51 99 70 0 235 242 33 123 127 31 100 100 0 1.179 1.21 1.159 1.161 1.355 1.364 0.798 120 792 244 263 0.237 132 112 144 119 0 0.237

Total number of rows: 16416

Table truncated, full table size 2507 Kbytes.




Supplementary data files not provided
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