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Sample GSM98600 Query DataSets for GSM98600
Status Public on Sep 01, 2006
Title Rat neonatal cardiomyocytes, AngII-Cy5 vs Prorenin-Cy3, dye-swap, slide_08,
Sample type RNA
 
Channel 1
Source name Rat neonatal cardiomyocytes, Ang-Cy5
Organism Rattus norvegicus
Characteristics Rat neonatal cardiomyocytes, AngII (100nM) 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, 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 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 28, 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
1 150 3616 3356 2955 99 101 10 100 100 0 2020 2315 2065 68 69 16 100 98 0 1.802 1.449 1.406 1.39 1.526 1.445 0.979 156 1109 5469 5504 0.849 3517 1952 3257 2247 0 0.849
2 120 7338 5471 3970 103 107 18 100 100 0 4183 3084 2196 73 75 12 100 99 0 1.76 1.783 1.729 1.727 1.558 1.807 0.973 120 808 11345 8379 0.816 7235 4110 5368 3011 0 0.816
3 90 1505 1506 201 90 91 16 100 100 0 2738 2694 325 58 61 29 100 100 0 0.528 0.537 0.54 0.537 1.119 0.536 0.954 52 420 4095 4052 -0.921 1415 2680 1416 2636 0 -0.921
4 80 287 282 33 97 98 9 100 100 0 449 442 56 76 77 8 100 100 0 0.509 0.505 0.503 0.501 1.22 0.5 0.933 52 340 563 551 -0.973 190 373 185 366 0 -0.973
5 100 719 675 226 104 107 17 100 98 0 552 526 151 89 92 17 100 100 0 1.328 1.307 1.324 1.231 1.374 1.348 0.971 80 560 1078 1008 0.41 615 463 571 437 0 0.41
6 110 226 247 111 96 97 10 100 98 0 286 268 63 70 71 7 100 100 0 0.602 0.763 0.635 0.668 1.496 0.967 0.716 80 656 346 349 -0.733 130 216 151 198 0 -0.733
7 100 119 117 15 103 104 13 57 25 0 110 108 23 81 82 11 73 56 0 0.552 0.519 0.588 0.566 2.007 0.572 0.393 80 560 45 41 -0.858 16 29 14 27 -50 null
8 80 206 214 40 103 106 14 98 98 0 145 147 20 80 82 11 100 100 0 1.585 1.657 1.702 1.614 1.511 1.835 0.809 52 340 168 178 0.664 103 65 111 67 0 0.664
9 80 155 155 20 96 97 9 100 100 0 128 130 16 68 69 8 100 100 0 0.983 0.952 0.92 0.934 1.344 0.957 0.747 52 340 119 121 -0.024 59 60 59 62 0 -0.024
10 90 542 518 86 98 99 11 100 100 0 347 340 42 69 70 8 100 100 0 1.597 1.55 1.574 1.535 1.139 1.591 0.955 52 420 722 691 0.675 444 278 420 271 0 0.675
11 80 735 732 69 102 106 65 100 100 0 378 370 43 70 71 8 100 100 0 2.055 2.1 2.094 2.107 1.116 2.222 0.89 52 340 941 930 1.039 633 308 630 300 0 1.039
12 90 365 352 79 92 92 8 100 100 0 361 354 41 64 64 12 100 100 0 0.919 0.897 0.906 0.858 1.327 0.957 0.918 52 420 570 550 -0.122 273 297 260 290 0 -0.122
13 70 125 127 13 95 96 7 100 93 0 96 98 12 67 67 6 100 96 0 1.034 1.032 1.074 1.057 1.569 1.136 0.531 32 236 59 63 0.049 30 29 32 31 0 0.049
14 90 167 167 20 98 98 8 100 100 0 91 92 9 69 69 5 94 94 0 3.136 3 3.065 3.044 1.673 3.153 0.643 52 420 91 92 1.649 69 22 69 23 0 1.649
15 80 112 112 10 94 94 7 90 65 0 90 90 8 70 70 6 94 82 0 0.9 0.9 0.886 0.858 2.328 1.215 0.363 52 340 38 38 -0.152 18 20 18 20 0 -0.152
16 100 421 428 79 102 102 9 100 100 0 401 378 72 77 78 8 100 100 0 0.985 1.083 1.072 1.092 1.228 1.075 0.939 80 560 643 627 -0.022 319 324 326 301 0 -0.022
17 100 1345 1277 254 102 105 14 100 100 0 544 519 94 72 74 11 100 100 0 2.633 2.629 2.607 2.601 1.26 2.659 0.968 80 560 1715 1622 1.397 1243 472 1175 447 0 1.397
18 100 1006 927 247 95 95 9 100 100 0 511 479 120 67 67 8 100 100 0 2.052 2.019 2.055 2.019 1.266 2.059 0.951 80 560 1355 1244 1.037 911 444 832 412 0 1.037
19 100 209 211 25 109 120 41 100 73 0 159 163 17 90 97 27 100 90 0 1.449 1.397 1.399 1.388 1.279 1.582 0.771 80 560 169 175 0.535 100 69 102 73 -50 null
20 140 543 980 1243 154 482 1098 15 9 0 248 279 103 103 158 176 30 6 0 2.683 4.693 2.745 3.198 1.768 10.191 0.445 156 989 534 1002 1.424 389 145 826 176 -100 null

Total number of rows: 16416

Table truncated, full table size 2425 Kbytes.




Supplementary data files not provided
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